1

When they jump the freight train, Kevin Flynn starts to repair Quorra. This seems to be just a normal thing in repairing a program, but in the middle of doing so, Sam says is looking at the code which looks like some sort of digital DNA,

She's an ISO

How does he know that she is an ISO just by looking at something he obviously has never seen before?

3

The previous line was a bit of a giveaway.

Flynn: I've got to identify the damaged code. The sequencing is just enormously complex.

Sam: But didn't you write it?

Flynn: Some of it. The rest of it is just beyond me.

especially given that he's already talked about the ISOs emerging from chaos

Sam: And you created them?

Flynn: No. No. They manifested, like a flame.

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