Search for CRISPR target site with micro-homology sequences

Data Input & Configuration Options

Sequence File Upload


This program shows the micro homology sequences striding over the double strand break (DSB) point created by CRISPR/Cas9 system.
In the repairing process of DSB with microhomology-mediated end joining (MMEJ), microhomologous sequences are thought to be aligned to join the broken ends, resulting deletion of a spacer region and a microhomologous sequence. (McVey & Lee 2008)
With this program you can predict the deletion pattern.

Enter the query sequence and select the number of homologous nucleotides.
In the result of "marked sequences", the mark " | " indicates the cleavage site and the mark " [NN..]" indicates the micro homology sequence.

In the right end column, the remainder after dividing the nt number of predicted deletion by three is shown.
This number helps to select frame shift mutation in your target gene.

The PAM seq (NGG) exists in the 3'-franking of 4-6 nt from the mark " | ".

Output sample

Analysis result

21     24..26     GCC[TCC]TCGTTCTCCA|[TCC]CGGAG   37..39     1
21     33..35     GCCTCCTCGTTC[TCC]A|[TCC]CGGAG   37..39     1
29     36..38     GTTCTCC[ATC]CCGGAG|G[ATC]GGTT   46..48     1
29     40..42     GTTCTCCATCC[CGG]AG|GAT[CGG]TT   48..50     2
29     29..31     [GTT]CTCCATCCCGGAG|GATCG[GTT]   50..52     0
48     48..50     [CGG]TTTCGCCGTCAGC|CTG[CGG]GG   67..69     1