public static void main(String[] args) {
		//first do global alignment bet gene and gen#0.
		readFile();
		int rows=gene.length()+1;//gene on left of table(rows).need +1 for start cell
		int cols=gen[0].length()+1;//genome on top. these values start@1
		table=new int[rows][cols];//allocates a large amt. of memory.
		for(int i=1;i<rows;i++){
			table[i][0]=i*-2;
		}
		for(int i=0;i<cols;i++){//iterate start cell w/ run
			table[0][i]=i*-2;
		}
		table[0][0]=0;//begin point
		int score=fillTable(rows,cols,0,cols-1);
		msg.println("score= "+score);
		String result=traceback(rows, cols, 0, 0);
//		printBoard(table);
		msg.println("Final Alignment:\n"+result);
		msg.println(gene);
		for(int i=0;i<5;i++){
			
			msg.println(gen[i]);
		}
	}