Assume the markov region is R and R[i] is the i-th char in the chain. The parameter of order-1 markov model 
consists of two parts. One is the initial probability which is a 1*4 vector and the other is the tansfer 
probability which is a 4*4 matrix.
A typical description of an order-1 markov model is

Pr(R[0]=A)
Pr(R[0]=C)
Pr(R[0]=G)
Pr(R[0]=G)

Pr(R[1]=A|R[0]=A)
Pr(R[1]=C|R[0]=A)
Pr(R[1]=G|R[0]=A)
Pr(R[1]=T|R[0]=A)
Pr(R[1]=A|R[0]=C)
Pr(R[1]=C|R[0]=C)
Pr(R[1]=G|R[0]=C)
Pr(R[1]=T|R[0]=C)
Pr(R[1]=A|R[0]=G)
Pr(R[1]=C|R[0]=G)
Pr(R[1]=G|R[0]=G)
Pr(R[1]=T|R[0]=G)
Pr(R[1]=A|R[0]=T)
Pr(R[1]=C|R[0]=T)
Pr(R[1]=G|R[0]=T)
Pr(R[1]=T|R[0]=T)