CRISPR Editing Target Design
Input a Gene ID, CDS, cDNA, or DNA sequence to rapidly rank SpCas9 (NGG PAM) candidate targets with published on-page rules. The page reports targets and scores only; it does not generate vector-specific primers or claim experimental editing efficiency.
TkA01G000070 · TK1151 · CDS 1170 bp
The example uses the site’s TK1151 reference CDS; the gene card provides identity and reference details.
Algorithm, scoring and interpretation
Up to 250,000 bp per query. Both strands of the entire accepted sequence are scanned; longer inputs are explicitly rejected. Ambiguous bases are preserved and input is not silently truncated.
Design and Scoring Rules
The tool scans both strands for a 20-nt guide adjacent to an SpCas9 NGG PAM. The cut site is reported 3 bp upstream of PAM. Scores are bounded from 0 to 100 and are used only to prioritize candidates within this tool.
| Component | Rule and points |
|---|---|
| Base and GC balance | Base 38 plus max(0, 24 − 1.15 × |GC% − 50|); GC closest to 50% receives up to 24 points. |
| PAM / 5′ preference | An NGG PAM adds 10; a guide beginning with G adds 6; an early input-sequence position adds 0–18 to favor candidates near the 5′ end of a gene or CDS/cDNA. |
| Sequence penalties | Subtract 12 for TTTT and 8 for any homopolymer of 5 or more bases. The final score is clipped to 0–100. |
This is a reproducible sequence-priority rule, not an in vivo editing-efficiency or off-target-risk prediction. Vector, promoter, delivery, and off-target validation must be determined for the specific experimental system.
Candidate Targets
No result yet; enter a Gene ID or valid DNA sequence.