How much sequence consensus do I need between homology arms and genome sequence for HDR?

11 July 2019 0 3K Report

I received a plasmid with two homology arms (5' = 510bp and 3' = 1012bp) that I would like to use for homologous recombination with the Cas9 enzyme.

I BLASTed the sequence of my homology arms to the species genome and found the 5' HA has 100% alignment with the gene sequence but the 3' HA has 98.91% alignment.

The gene sequence is 1005bp, and my HA has 1012bp. So there are +6 additional bps added to my HA sequence. I also noticed there are 5 sites of bp mismatch between the HA and the gene. I've attached an image of the alignment results.

Is 98.91% sequence consensus okay for my HA to be used in homologous recombination? Or should I have 100% sequence consensus?

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