DNA pattern: figure 4.1

size = 60000
nr = (dnalen %/% size) + as.numeric((dnalen %% size)>0) # number of horiz lines, accord to _size_
plot(x=c(1,size), y=c(nr,nr), type="l", xlab="", ylab="", ylim=c(0,nr), axes=F, col=par()$bg)
axis(1, at=seq(0,60000,10000), labels=paste(seq(0,60,10),"K", sep=""), tcl=0.5)

for(curr_row in 1:nr) {
# the horizontal line
segsize=size
begin = seq(from = 1, to=dnalen, by=size)[curr_row]
if((begin+size)>dnalen) {
segsize = dnalen-begin+1
}
lines(x=c(1,segsize), y=c(nr-curr_row+1, nr-curr_row+1), type="l")

# the vertical "tick"s for location of palindrome
pos.begin = (curr_row-1)*size+1 # beginning of the row
pos.end = pos.begin+segsize-1 # end of the row
pal.loc = posvec[posvec>pos.begin & posvec <= pos.end] # locations
pal.loc = pal.loc - size*(curr_row-1) # shift locations

for(i in 1:length(pal.loc)) {
lines(x=c(pal.loc[i],pal.loc[i]), y=c(nr-curr_row+1-0.1,nr-curr_row+1+0.1))
}
}