Suppose I have two vectors of length 25, and I want to compute their covariance matrix. I try doing this with numpy.cov, but always end up with a 2x2 matrix.
As pointed out above, you only have two vectors so you'll only get a 2x2 cov matrix.
IIRC the 2 main diagonal terms will be sum( (x-mean(x))**2) / (n-1) and similarly for y.
The 2 off-diagonal terms will be sum( (x-mean(x))(y-mean(y)) ) / (n-1). n=25 in this case.