Which reference genome should the designs target?
Indices are pre-built for each organism's individual gene sequences
Enter one or more
FASTA format sequences to evaluate e.g:

>some sequence
The file should contain
FASTA format sequences to evaluate e.g:

>some sequence
Should the CRISPR designs should be checked for any secondary off-target effects.
This means if they will cut in any exogenous, foreign introduced sequences.
Select individual off-targets from the list or paste a set of fasta sequences into the text area
This text area only accepts FASTA format sequences as input e.g.:
>some sequence
Design of CRISPR constructs
Design Evaluation MultiCRISP CLD GenomeCRISPR Help Links

Check out our new CRISPR Library Designer (CLD): batch design of sgRNA libraries
Download the dockerized version now at CLD on Github

1. Select organism:


Number of 5' mismatch positions ignored by the programm.

Tolerated edit distance to the target sequence

2. Enter target sequence:

FASTA example [HELP]

Please enter the target sequence without the PAM. In FASTA a format e.g:

>some sequence
All possible PAMs will be added during the search process.

Alternatively upload a file in FASTA format or a new line separated list of gene symbols and/or accesion numbers


The older version of E-CRISP can be reached Here

Boutros lab, E-CRISP-Version 5.3
For suggestions please contact us at crispr@dkfz.de