Indicate which reference genome E-CRISP should find targets in?
Indices are pre-built for each organisms individual gene sequences
Enter either:

a ";" separated list of official gene symbols or Accession IDs. For e.g.

ENSDARG00000090752;ENSDARG00000063570;ENSDARG00000074914;ENSDARG00000032801 (for Zebrafish)
FBgn0000442;FBgn0250906;FBgn0020618;FBgn0044323 (for Fly)


one or more Fasta formatted sequence. For e.g:


Transcript IDs (ENST...) can be entered in subsection 4
but still require the respective gene to be entered here.
Maximum length of the sgRNA target site (protospacer)
Minimum length of the sgRNA target site (protospacer)
Adjust the length of the sequence that will be saved 3' to the cut site.
Adjust the length of the sequence that will be saved 5' to the cut site.
TTTT motifs can hinder RNA transcription. Thus it can be wise to exclude target sites harboring such motifs.
Target only inside the gene of interest.
Else designs can also be up to 500 bp up-/or downstream of the desired gene.
Check if designs should only target exons.
Check if designs should target only outside of predicted CpG islands.
(Outside potential hypermethylated regions)
Enter a specific ensembl transcript ID ENSTR.......
Enter the exon number to target. E.g. Enter 1 to find designs which target the first exon exon.
Or enter the word any to find designs that hit any exon.
Check this box to assess restricion enzyme cut sites in the whole target sequence.
Choose between different pre-defined restriction enzyme subsets.
Leave this box checked if designs should be analysed for targets in the reference genome.
Should the CRISPR design be checked for any secondary off-target effects?
This is useful to check if they will cut in any exogenous, foreign introduced sequence.
Check every individual off-target 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:


2. Select target region by gene symbol or sequence:

Input is GeneSymbol
Input is FASTA sequence

FASTA example | GeneSymbol example | Clear [HELP]

3. Start application:

(any PAM (NAG/NGG...), any 5' base (A,C,G,T,...), off-targets need full length perfect match, introns are allowed)

(any PAM (NAG/NGG...), any 5' base (A,C,G,T,...), off-targets tolerate mismatches, introns/CPG islands are excluded)

(only NGG PAM, only G as 5' base, off-target tolerates many mismatches and ignores non-seed region, introns, purpose is knockout (only first 3 coding exons are allowed) and UTRs are excluded)

The older version of E-CRISP can be reached Here

Boutros lab, E-CRISP-Version 5.4
For suggestions please contact us at