\begin{Verbatim}[commandchars=\\\{\}]
\PYG{k+kn}{import} \PYG{n+nn}{pylab}

\PYG{n}{pylab}\PYG{o}{.}\PYG{n}{cla}\PYG{p}{()}  \PYG{c+c1}{\PYGZsh{} clear any prior graph}
\PYG{n}{pylab}\PYG{o}{.}\PYG{n}{gray}\PYG{p}{()}
\PYG{n}{pylab}\PYG{o}{.}\PYG{n}{scatter}\PYG{p}{(}\PYG{n}{x}\PYG{p}{,} \PYG{n}{y}\PYG{p}{)}
\PYG{n}{pylab}\PYG{o}{.}\PYG{n}{xlim}\PYG{p}{(}\PYG{l+m+mi}{0}\PYG{p}{,} \PYG{n+nb}{len}\PYG{p}{(}\PYG{n}{rec\PYGZus{}one}\PYG{p}{)} \PYG{o}{\PYGZhy{}} \PYG{n}{window}\PYG{p}{)}
\PYG{n}{pylab}\PYG{o}{.}\PYG{n}{ylim}\PYG{p}{(}\PYG{l+m+mi}{0}\PYG{p}{,} \PYG{n+nb}{len}\PYG{p}{(}\PYG{n}{rec\PYGZus{}two}\PYG{p}{)} \PYG{o}{\PYGZhy{}} \PYG{n}{window}\PYG{p}{)}
\PYG{n}{pylab}\PYG{o}{.}\PYG{n}{xlabel}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s+s2}{ (length }\PYG{l+s+si}{\PYGZpc{}i}\PYG{l+s+s2}{ bp)\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{rec\PYGZus{}one}\PYG{o}{.}\PYG{n}{id}\PYG{p}{,} \PYG{n+nb}{len}\PYG{p}{(}\PYG{n}{rec\PYGZus{}one}\PYG{p}{)))}
\PYG{n}{pylab}\PYG{o}{.}\PYG{n}{ylabel}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s+s2}{ (length }\PYG{l+s+si}{\PYGZpc{}i}\PYG{l+s+s2}{ bp)\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{rec\PYGZus{}two}\PYG{o}{.}\PYG{n}{id}\PYG{p}{,} \PYG{n+nb}{len}\PYG{p}{(}\PYG{n}{rec\PYGZus{}two}\PYG{p}{)))}
\PYG{n}{pylab}\PYG{o}{.}\PYG{n}{title}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}Dot plot using window size }\PYG{l+s+si}{\PYGZpc{}i}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s+s2}{(allowing no mis\PYGZhy{}matches)\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{window}\PYG{p}{)}
\PYG{n}{pylab}\PYG{o}{.}\PYG{n}{show}\PYG{p}{()}
\end{Verbatim}
