You might have a look at the seqinr package.

This will give you a dot plot, though it uses boxes instead of dots.

library(seqinr)
help(dotPlot)
example(dotPlot)

And with your example:

dotPlot(seq1=strsplit("ATGCTAC","")[[1]],seq2=strsplit("ATCAGAT","")[[1]])

Here's an ascii answer in python for kicks:

import sys

def draw(A, B):
    return " %s\n" % A + "\n".join(b + "".join("\x1B[42m \x1b[0m" \
           if a == b else "\x1B[41m \x1B[0m" for a in A) for b in B)

print draw(sys.argv[1], sys.argv[2])

If you call it like:

python ansidot.py ATGCTAC ATCAGAT

It gives ascii output like: