Search for CRISPR target site with micro-homology sequences
Data Input & Configuration Options
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
Output |
---|
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 ... |