TURBOTHINK
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Yes they would know. There would be more than the normal amount of markers in common between mom and daughter. This would show that a blood relative of mom's is the father.
That's the easiest way to explain it without getting really technical and scientific - had to ask my son to explain it to me in English because the first time he told me I was lost by the 4th word! (he's Biology/Chemistry employed in AL by gov't agency).
I am sure they have to have gotten full DNA profile though - everyone obsesses about the hair in the trunk that didn't have a skin tag for full DNA analysis. I ask, what about the stain!! It was body fluids - they have toothbrushes and hairbrushes and dirty clothes - I am sure they have Caylee's full DNA profile! It just might have taken longer to get given that CA gave them the wrong hairbrush, etc...
They had Caylee's complete DNA profile from the testing JG had done. That was really not an issue. It is very simple to determine incest in a DNA profile (simple explanation)because the "father" markers are totally different than the "mother" markers in a normal DNA. Both have their family markers.
If there is incest the "father" markers would have the same DNA markers as the mother. To determine between LA & GA would get a little more complicated, and that may be why they asked both for their DNA including CA. They would "remove" the similar markers and see what was left.(which person's )