// alignments from the full model

Include T0172.t2k.undertaker-align.script 
ReadFragmentAlignment T0172.t2k-2track-undertaker.a2m


InfilePrefix 1dusA/
   include read-alignments.under
InfilePrefix 1dl5A/
   include read-alignments.under
InfilePrefix 1i9gA/
   include read-alignments.under
InfilePrefix 1xvaA/
   include read-alignments.under
InfilePrefix 1g38A/
   include read-alignments.under
InfilePrefix 2admA/
   include read-alignments.under
InfilePrefix 1jg1A/
   include read-alignments.under
InfilePrefix 1bhjA/
   include read-alignments.under
InfilePrefix 1kpgA/
   include read-alignments.under
InfilePrefix 1g6q2/
   include read-alignments.under

InfilePrefix