\begin{Verbatim}[commandchars=\\\{\}]
\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}{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}{3.0}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{alignments} \PYG{o}{=} \PYG{n}{aligner}\PYG{o}{.}\PYG{n}{align}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}DEHEK\PYGZdq{}}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}DHHKK\PYGZdq{}}\PYG{p}{)}
\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}{DEHEK}
\PYG{g+go}{|.|.|}
\PYG{g+go}{DHHKK}
\PYG{g+go}{\PYGZlt{}BLANKLINE\PYGZgt{}}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{print}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}.2f}\PYG{l+s+s2}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{alignments}\PYG{o}{.}\PYG{n}{score}\PYG{p}{)}
\PYG{g+go}{\PYGZhy{}2.18}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{score} \PYG{o}{=} \PYG{n}{m}\PYG{p}{[}\PYG{l+s+s1}{\PYGZsq{}D\PYGZsq{}}\PYG{p}{,}\PYG{l+s+s1}{\PYGZsq{}D\PYGZsq{}}\PYG{p}{]} \PYG{o}{+} \PYG{n}{m}\PYG{p}{[}\PYG{l+s+s1}{\PYGZsq{}E\PYGZsq{}}\PYG{p}{,}\PYG{l+s+s1}{\PYGZsq{}H\PYGZsq{}}\PYG{p}{]} \PYG{o}{+} \PYG{n}{m}\PYG{p}{[}\PYG{l+s+s1}{\PYGZsq{}H\PYGZsq{}}\PYG{p}{,}\PYG{l+s+s1}{\PYGZsq{}H\PYGZsq{}}\PYG{p}{]} \PYG{o}{+} \PYG{n}{m}\PYG{p}{[}\PYG{l+s+s1}{\PYGZsq{}E\PYGZsq{}}\PYG{p}{,}\PYG{l+s+s1}{\PYGZsq{}K\PYGZsq{}}\PYG{p}{]} \PYG{o}{+} \PYG{n}{m}\PYG{p}{[}\PYG{l+s+s1}{\PYGZsq{}K\PYGZsq{}}\PYG{p}{,}\PYG{l+s+s1}{\PYGZsq{}K\PYGZsq{}}\PYG{p}{]}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{print}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}.2f}\PYG{l+s+s2}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{score}\PYG{p}{)}
\PYG{g+go}{\PYGZhy{}2.18}
\end{Verbatim}
