CRISPOR (
citation
) is a program that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system.
CRISPOR Manual
July 2025: Added hasCas12Max and e-SpotOn. Also allowing old primer links to Crispor to work again. See
Full list of changes
Step 1
Sequence name (optional):
Enter a single genomic sequence, < 2300 bp, typically an exon
Clear Box
-
Reset to default
ATTCTACTTTTCAACAATAATACATAAACatattggcttgtggtagCAACACTATCATGGTATCACTAACGTAAAAGTTCCTCAATATTGCAATTTGCTTGAACGGATGCTATTTCAGAATATTTCGTACTTACACAGGCCATACATTAGAATAATATGTCACATCACTGTCGTAACACTCT
Text case is preserved, e.g. you can mark ATGs with lowercase.
Instead of a sequence, you can paste a chromosome range, e.g. chr1:11,130,540-11,130,751
Step 2
Select a genome
-- No Genome: no specificity, only cleavage efficiency scores (max. len 25kbp)
Vitis vinifera - Chardonnay cl. R8 - v1.0
Vitis vinifera - Thompson Seedless FPS02A - v1.0
Note: pre-calculated exonic guides for this species are on the
UCSC Genome Browser
.
Step 3
Select a Protospacer Adjacent Motif (PAM)
20bp-NGG - Sp Cas9, SpCas9-HF1, eSpCas9 1.1
20bp-NNG - Cas9 S. canis
20bp-NGN - SpG
20bp-NNGT - Cas9 S. canis - high efficiency PAM, recommended
20bp-NAA - iSpyMacCas9
TTN-23bp - hfCas12Max - as recommended by Synthego
TNN-23bp - hfCas12Max, broader PAM, as recommended by Synthego
NGG-22bp - eSpOT-ON (ePsCas9), as recommended by Synthego
21bp-NNG(A/G)(A/G)T - Cas9 S. Aureus
20bp-NNG(A/G)(A/G)T - Cas9 S. Aureus with 20bp-guides
20bp-NG(G/T) - xCas9, recommended PAM, see notes
21bp-NNN(A/G)(A/G)T - KKH SaCas9
20bp-NNN(A/G)(A/G)T - KKH SaCas9 with 20bp-guides
20bp-NGA - Cas9 S. Pyogenes mutant VQR
24bp-NNNNCC - Nme2Cas9
20bp-NGCG - Cas9 S. Pyogenes mutant VRER
20bp-NNAGAA - Cas9 S. Thermophilus
20bp-NGGNG - Cas9 S. Thermophilus
20bp-NNNNG(A/C)TT - Cas9 N. Meningitidis
20bp-NNNNACA - Cas9 Campylobacter jejuni, original PAM
22bp-NNNNRYAC - Cas9 Campylobacter jejuni, revised PAM
22bp-NNNVRYAC - Cas9 Campylobacter jejuni, opt. efficiency
TTCN-20bp - CasX
TTT(A/C/G)-23bp - Cas12a (Cpf1) - recommended, 23bp guides
TTT(A/C/G)-21bp - Cas12a (Cpf1) - 21bp guides recommended by IDT
TTTN-23bp - Cas12a (Cpf1) - low efficiency
ATTN-23bp - BhCas12b v4
NGTN-23bp - ShCAST/AcCAST, Strecker et al, Science 2019
T(C/T)C(A/C/G)-23bp - TYCV As-Cpf1 K607R
TAT(A/C/G)-23bp - TATV As-Cpf1 K548V
TTTA-23bp - TTTA LbCpf1
TCTA-23bp - TCTA LbCpf1
TCCA-23bp - TCCA LbCpf1
CCCA-23bp - CCCA LbCpf1
GGTT-23bp - CCCA LbCpf1
YTTV-20bp - MAD7 Nuclease, Lui, Schiel, Maksimova et al, CRISPR J 2020
TTYN- or VTTV- or TRTV-23bp - enCas12a E174R/S542R/K548R - Kleinstiver et al Nat Biot 2019
20bp-NNNNCNAA - Thermo Cas9 - Walker et al, Metab Eng Comm 2020
20bp-NNN - SpRY, Walton et al Science 2020
20bp-NRN - SpRY (high efficiency PAM)
20bp-NYN - SpRY (low efficiency PAM)
See
notes on enzymes
in the manual.
Version 5.2 -
Documentation
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Citation
-
License
CRISPR/Cas9 Guide Designer for chordate vertebrate ecdysozoans lophotrochozoans protostomes spongi corals plants butterflies metazoans genomes fruitflies insects nematodes mammals.
