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\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{k+kn}{from} \PYG{n+nn}{Bio.Seq} \PYG{k+kn}{import} \PYG{n}{reverse\PYGZus{}complement}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{seq1} \PYG{o}{=} \PYG{l+s+s2}{\PYGZdq{}AAAACCC\PYGZdq{}}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{seq2} \PYG{o}{=} \PYG{l+s+s2}{\PYGZdq{}AACC\PYGZdq{}}
\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}{mismatch\PYGZus{}score} \PYG{o}{=} \PYG{o}{\PYGZhy{}}\PYG{l+m+mi}{1}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{aligner}\PYG{o}{.}\PYG{n}{internal\PYGZus{}gap\PYGZus{}score} \PYG{o}{=} \PYG{o}{\PYGZhy{}}\PYG{l+m+mi}{1}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{aligner}\PYG{o}{.}\PYG{n}{score}\PYG{p}{(}\PYG{n}{seq1}\PYG{p}{,} \PYG{n}{seq2}\PYG{p}{)}  \PYG{c+c1}{\PYGZsh{} strand is \PYGZdq{}+\PYGZdq{} by default}
\PYG{g+go}{4.0}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{aligner}\PYG{o}{.}\PYG{n}{score}\PYG{p}{(}\PYG{n}{seq1}\PYG{p}{,} \PYG{n}{reverse\PYGZus{}complement}\PYG{p}{(}\PYG{n}{seq2}\PYG{p}{),} \PYG{n}{strand}\PYG{o}{=}\PYG{l+s+s2}{\PYGZdq{}\PYGZhy{}\PYGZdq{}}\PYG{p}{)}
\PYG{g+go}{4.0}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{aligner}\PYG{o}{.}\PYG{n}{score}\PYG{p}{(}\PYG{n}{seq1}\PYG{p}{,} \PYG{n}{seq2}\PYG{p}{,} \PYG{n}{strand}\PYG{o}{=}\PYG{l+s+s2}{\PYGZdq{}\PYGZhy{}\PYGZdq{}}\PYG{p}{)}
\PYG{g+go}{0.0}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{aligner}\PYG{o}{.}\PYG{n}{score}\PYG{p}{(}\PYG{n}{seq1}\PYG{p}{,} \PYG{n}{reverse\PYGZus{}complement}\PYG{p}{(}\PYG{n}{seq2}\PYG{p}{))}
\PYG{g+go}{0.0}

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