transmatp<-function(sites,col,matrix0){
#sites = numeric matrix of n binding sites, w positions
#col = column that transition matrix produces
#matrix0 = matrix of counts for n = col, initialized to 0
matrixn<-matrix0
for(i in 1:length(sites[,1])){
j<-sites[i,(col-1)]
matrixn[j,sites[i,col]]<-matrixn[j,sites[i,col]]+1
}
#Change counts to probabilities
matrixp<-matrixn
matrixp<-matrixp+1 #Adds 1 to every element
for(i in 1:4){
matrixp[i,]<-matrixp[i,]/sum(matrixp[i,])
#Denominator=sum(matrixn[i,])+4
}
return(matrixp, matrixn)
}