\relax 
\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces Comparison of candidate ../1ba1/1ba1-T0089-global.pw.a2m (lines) to reference ../1ba1/T0089-1ba1-2track-global.pw.a2m (letters). Reference alignment has 321 matching columns, Candidate alignment has 307 matching columns. 32 were used (for template shift+target shift) to compute shift score. The shift score is 0.005988, with a min shift of 167, max shift of 0, and mean of 0.000000. Optimal subalignment has 166 matching columns, with 238 paired matches. 1 were used (for template shift+target shift) to compute shift score. Optimum shift score is 0.542915, with a min shift of 545, max shift of 0, and mean of 2.895779. Optimum achieved by removing the 212 columns indicated with dotted lines from the candidate alignment. }}{1}}