\begin{Verbatim}[commandchars=\\\{\}]
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{from} \PYG{n+nn}{Bio} \PYG{k+kn}{import} \PYG{n}{Align}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{aligner} \PYG{o}{=} \PYG{n}{Align}\PYG{o}{.}\PYG{n}{PairwiseAligner}\PYG{p}{()}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{aligner}\PYG{o}{.}\PYG{n}{substitution\PYGZus{}matrix} \PYG{o}{=} \PYG{n}{m}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{aligner}\PYG{o}{.}\PYG{n}{gap\PYGZus{}score} \PYG{o}{=} \PYG{o}{\PYGZhy{}}\PYG{l+m+mf}{1.0}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{s1} \PYG{o}{=} \PYG{p}{(}\PYG{l+s+s1}{\PYGZsq{}AAT\PYGZsq{}}\PYG{p}{,} \PYG{l+s+s1}{\PYGZsq{}CTG\PYGZsq{}}\PYG{p}{,} \PYG{l+s+s1}{\PYGZsq{}TTT\PYGZsq{}}\PYG{p}{,} \PYG{l+s+s1}{\PYGZsq{}TTT\PYGZsq{}}\PYG{p}{)}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{s2} \PYG{o}{=} \PYG{p}{(}\PYG{l+s+s1}{\PYGZsq{}AAT\PYGZsq{}}\PYG{p}{,} \PYG{l+s+s1}{\PYGZsq{}TTA\PYGZsq{}}\PYG{p}{,} \PYG{l+s+s1}{\PYGZsq{}TTT\PYGZsq{}}\PYG{p}{)}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{alignments} \PYG{o}{=} \PYG{n}{aligner}\PYG{o}{.}\PYG{n}{align}\PYG{p}{(}\PYG{n}{s1}\PYG{p}{,} \PYG{n}{s2}\PYG{p}{)}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{len}\PYG{p}{(}\PYG{n}{alignments}\PYG{p}{)}
\PYG{g+go}{2}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{print}\PYG{p}{(}\PYG{n}{alignments}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{])}
\PYG{g+go}{AAT CTG TTT TTT}
\PYG{g+go}{||| ... ||| \PYGZhy{}\PYGZhy{}\PYGZhy{}}
\PYG{g+go}{AAT TTA TTT \PYGZhy{}\PYGZhy{}\PYGZhy{}}
\PYG{g+go}{\PYGZlt{}BLANKLINE\PYGZgt{}}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{print}\PYG{p}{(}\PYG{n}{alignments}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{])}
\PYG{g+go}{AAT CTG TTT TTT}
\PYG{g+go}{||| ... \PYGZhy{}\PYGZhy{}\PYGZhy{} |||}
\PYG{g+go}{AAT TTA \PYGZhy{}\PYGZhy{}\PYGZhy{} TTT}
\PYG{g+go}{\PYGZlt{}BLANKLINE\PYGZgt{}}
\end{Verbatim}
