Why the Guide RNA sequence suggested are not the same as the target region ?

I have a project concerning BRCA1 knockout,

by using crispr.mit.edu tool (V2), I cannot find a gRNA that matches perfectly my target sequence.

I'va selected the whole BRCA1 gene and selected the first 3 exons to do a cas9 assay.

The first 2 guides show a score of 99%, which is good but the sequence simply is not the same à the exon targeted sequence,

do you have an explanation for that ?

Despite the 99% score I'm not confortable with the fact that my guide won't be as same as the targeted genome sequence.

Here is the example :

Guide info

CRISPR tool type cas9


5' pam sequence (N/A)

3' pam sequence TGG

target exon name EXON_1

target exon start BRCA1 3348

on-target strand 1

predicted off-targets


Hsu, 2013 score 99.85011394611143

On-target cut site


On-target exon sequence



Off-target predictions

offtarget positionmismatches
NC_000021.9 38519815 +14:T>C,16:G>C,18:T>A
NC_000011.10 98392516 +6:A>T,7:A>G,8:A>C
NC_000016.10 87203142 +4:A>G,15:C>A,19:A>T

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Lavender Trollabout 4 years ago

That site is showing you off-target regions in the genome.
It is showing you other regions in the genome that might be targeted by your guide.
99 is a good score with few off target sequences.

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