DNA pattern: sliding window

######################
# Sliding window approach for finding the largest cluster
# interval size 1000 bp
# overlap of 500 bp
######################

winLen = 1000
overlap = 500
begins = seq(from=1, to=dnalen-winLen+1, by=overlap) # for storing the palindrome counts
numPals = rep(NA, length(begins))
for(i in 1:length(begins)) {
numPals[i]=sum(begins[i]:(begins[i]+winLen-1) %in% posvec)
cat(i, "\t", begins[i], "\n")
}
plot(numPals, type="l", xlab="Position of window (base pairs)", ylab="Palindrome count")