\begin{Verbatim}[commandchars=\\\{\}]
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{alignments} \PYG{o}{=} \PYG{n}{pairwise2}\PYG{o}{.}\PYG{n}{align}\PYG{o}{.}\PYG{n}{localms}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}AGAACT\PYGZdq{}}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}GAC\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{5}\PYG{p}{,} \PYG{o}{\PYGZhy{}}\PYG{l+m+mi}{4}\PYG{p}{,} \PYG{o}{\PYGZhy{}}\PYG{l+m+mi}{2}\PYG{p}{,} \PYG{o}{\PYGZhy{}}\PYG{l+m+mf}{0.5}\PYG{p}{)}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{print}\PYG{p}{(}\PYG{n}{pairwise2}\PYG{o}{.}\PYG{n}{format\PYGZus{}alignment}\PYG{p}{(}\PYG{o}{*}\PYG{n}{alignments}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]))}
\PYG{g+go}{2 GAAC}
\PYG{g+go}{  | ||}
\PYG{g+go}{1 G\PYGZhy{}AC}
\PYG{g+go}{  Score=13}
\PYG{g+go}{\PYGZlt{}BLANKLINE\PYGZgt{}}
\end{Verbatim}
