Two tomoe will also allow the ninja to pierce Genjutsu and see the surrounding reality for what it really is. It can also allow the member to pierce another?s body and see their chakra. While the eye is not refined enough to see the tenketsu and chakra circulatory system like the Byakugan, it can view the movement and flow of chakra. This can help them tell if a person is trapped in a Genjutsu, or if an attacker is a real threat or merely a bunshin.
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obvisly rei has more than two tomoe, so she can see right through your genjutsu
but I didnt think you needed line of sight to use your genjutsu, I was under the impression that people could use genjutsu as long as they made the seals, sharingan doesnt need seals(I think), but i think thats why they require you to have line of sight, because the eye itself does the genjutsu.