Eukaryotic Pathogen CRISPR gRNA Design Tool

with (1) custom genome upload, (2) off-target analysis, (3) on-targets searching (for targeting gene families), (4) efficiency/activity prediction, (5) assisted oligo repair template design , (6) gRNA transcription problem identification, (7) flanking microhomology searching (for predicting deletions)

  Paste one sequence in FASTA format or plain sequence (no headers)
  For identifying gRNA hitting multiple members in a gene family, we recommend first conducting a multiple sequence alignment of your gene family, select a few genes that have high homology to the alignment consensus, then with which run our program and compare the results.

  Please select a genome from the list. You can also upload your custom genome sequence in FASTA format, 200MB file size limit. If you have a frequently used genome or a large genome you would like to add to our server, please contact duopeng[at]

  Computation progress will be actively updated, results will be displayed once computation is completed. Results of each analysis are stored for a week, and can be access using the provided link.
  A summary table of ranked gRNA will be available in the results page, gRNAs are ranked by total score, the table also provides efficiency score, numbers of on and off-target, target score and flanking microhomology score for each gRNA. Our experimental data shows that the best gRNA for a gene usually falls in the high-scoring section of the ranked list, but there is no experimental data showing that all top-scoring gRNA will perform as expected.
  Detailed information of on and off-target hits (such as a list of all target positions in the genome, alignment quality, and corresponding annotations) will be accessible from links in the results page. Details of flanking microhomology will be accessible from a link in the results page

  gRNA is named by the position and strand in supplied sequence, (e.g. YourGene_170_revcom means a gRNA found at 170bp position on reverse-complementary strand of your gene)

  Google Chrome, Mozilla Firefox and Microsoft Internet Explorer are fully supported, Safari browser might experience problems with displaying schematic diagrams.