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\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{from} \PYG{n+nn}{Bio.Align} \PYG{k+kn}{import} \PYG{n}{PairwiseAligner}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{aligner} \PYG{o}{=} \PYG{n}{PairwiseAligner}\PYG{p}{()}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{aligner}\PYG{o}{.}\PYG{n}{mode} \PYG{o}{=} \PYG{l+s+s1}{\PYGZsq{}local\PYGZsq{}}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{aligner}\PYG{o}{.}\PYG{n}{match\PYGZus{}score} \PYG{o}{=} \PYG{l+m+mi}{2}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{aligner}\PYG{o}{.}\PYG{n}{mismatch\PYGZus{}score} \PYG{o}{=} \PYG{o}{\PYGZhy{}}\PYG{l+m+mi}{3}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{aligner}\PYG{o}{.}\PYG{n}{open\PYGZus{}gap\PYGZus{}score} \PYG{o}{=} \PYG{o}{\PYGZhy{}}\PYG{l+m+mi}{7}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{aligner}\PYG{o}{.}\PYG{n}{extend\PYGZus{}gap\PYGZus{}score} \PYG{o}{=} \PYG{o}{\PYGZhy{}}\PYG{l+m+mi}{2}
\end{Verbatim}
