private void alignmentPrint(String ref,int pID,int tID)
	{
		int patternInd=pID;
		int textInd=tID;
		String p="";
		String t="";
		String a="";
		for(int i=ref.length()-1;i>=0;i--)
		{
			if(ref.charAt(i)=='M' || ref.charAt(i)=='R')
			{
				p+=this.p[patternInd];
				t+=this.t[textInd];
				a+=ref.charAt(i);
				patternInd++;
				textInd++;
			}
			if(ref.charAt(i)=='I')
			{
				p+="-";
				t+=this.t[textInd];
				a+=ref.charAt(i);
				textInd++;
			}
			if(ref.charAt(i)=='D')
			{
				p+=this.p[patternInd];
				t+="-";
				a+=ref.charAt(i);
				patternInd++;
			}
		}
		System.out.println(p);
		System.out.println(t);
		System.out.println(a);
		}