\relax 
\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces Comparison of candidate ../1ba1/T0089-1ba1-local.pw.a2m (lines) to reference ../1ba1/T0089-1ba1-2track-global.pw.a2m (letters). Reference alignment has 321 matching columns, Candidate alignment has 326 matching columns. 27 were used (for template shift+target shift) to compute shift score. The shift score is 0.000000, with a min shift of 290, max shift of 0, and mean of 0.000000. Optimal subalignment has 290 matching columns, with 383 paired matches. 0 were used (for template shift+target shift) to compute shift score. Optimum shift score is 0.889437, with a min shift of 615, max shift of 0, and mean of 0.981420. Optimum achieved by removing the 129 columns indicated with dotted lines from the candidate alignment. }}{1}}