\relax 
\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces Comparison of candidate t49-2bltA-global.pw.a2m.gz (lines) to reference t49-2bltA-vast.a2m (letters). Reference alignment has 326 matching columns, Candidate alignment has 259 matching columns. 492 were used (for template shift+target shift) to compute shift score. The shift score is 0.656709, with a min shift of 0, max shift of 99, and mean of 5.472322. Optimal subalignment has 336 matching columns, with 202 paired matches. 404 were used (for template shift+target shift) to compute shift score. Optimum shift score is 0.721970, with a min shift of 0, max shift of 1, and mean of 0.094059. Optimum achieved by removing the 57 columns indicated with dotted lines from the candidate alignment. }}{1}}