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As for the plotting part, there is a points command that will do what you want. You'll want to zip up the points first, given its syntax.

Pts = zip(X,Y) # this should make a list of pairs from X and Y
points(Pts,size=10,color='red') # the command, with a couple standard options

I'm not sure if your other question is well-defined. Have you tried doing a linear regression? There are several ways to do this in Sage, though most of them require using one of its subpackages...