Hi,
for the cre lox system you usally use two times the same lox sequence (lox - gfp - lox e.g.)
However, there is a small chance of homologous recombination isn't it?
Here are described alternative sites (LoxN)
And as far as I understand, you could also make "LoxP - GFP - LoxN" whereby the lox'es have slightly different sequences.
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