//check mismatch primers

public class primer1Entry extends primerEntry
{
    int snploc = 0; 	//position of snp
    int misloc = 0; 	//position of mismatch
    int difLoc = 0; 	//distance of mismatch from snp
    int optTm = 0;	//optimum Tm
    int difTm = 0;	//difference between primer Tm and optimum Tm

    primer1Entry prev = null;
    primer1Entry next = null;

    public primer1Entry (String s, int p1, int p2, int p3, int p4, int p5, int p6)
    {
	super(s, p1, p2, p3);
	snploc = p4;
	misloc = p5;
	optTm = p6;
	if (end3 > misloc) difLoc = end3 - misloc;
	else difLoc = misloc - end3;
	if (optTm > tm) difTm = optTm - tm;
	else difTm = tm - optTm;
    }
}