w=4;  #position that exerts effect on other positions. 
N=1000; #number of signal examples in data set
r=10;	 # length of signal
data1<-matrix(nrow=N,ncol=r);
data1[]=runif(N*r,min=0,max=1);

	
#loops below generate data sequence randomly, but allowing for dependence on 
#position w

#the data will be contained in the matrix data1
  	
for(x1 in 1:N)
{
			if(data1[x1,w]<=0.25) data1[x1,w]="a"
			else if(data1[x1,w]<=0.5) data1[x1,w]="g"
			else if(data1[x1,w]<=0.75) data1[x1,w]="c"
			else data1[x1,w]="t"			
			for(x2 in 1:r)
			{	if(x2!=w)
				{	if(data1[x1,w]=="a")
					{	if(data1[x1,x2]<=0.25) data1[x1,x2]="a"
						else if(data1[x1,x2]<=0.5) data1[x1,x2]="g"
						else if(data1[x1,x2]<=0.75) data1[x1,x2]="c"
						else data1[x1,x2]="t"			
					}
					else if(data1[x1,w]=="g")
					{	if(data1[x1,x2]<=0.5) data1[x1,x2]="a"
						else if(data1[x1,x2]<=0.75) data1[x1,x2]="g"
						else if(data1[x1,x2]<=0.85) data1[x1,x2]="c"
						else data1[x1,x2]="t"			
					}
					else if(data1[x1,w]=="c")
					{	if(data1[x1,x2]<=0.05) data1[x1,x2]="a"
						else if(data1[x1,x2]<=0.75) data1[x1,x2]="g"
						else if(data1[x1,x2]<=0.85) data1[x1,x2]="c"
						else data1[x1,x2]="t"			
					}
					else if(data1[x1,w]=="t")
					{	if(data1[x1,x2]<=0.25) data1[x1,x2]="a"
						else if(data1[x1,x2]<=0.5) data1[x1,x2]="g"
						else if(data1[x1,x2]<=0.9) data1[x1,x2]="c"
						else data1[x1,x2]="t"			
					}
				}  #end if
			}#end x2 loop
}#end x1 loop