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revision 1.1, Mon Mar 8 21:43:51 2010 UTC revision 1.2, Mon Apr 12 20:27:23 2010 UTC
# Line 215  Line 215 
215      my @cand;      my @cand;
216      @cand = grep { $_->[2] =~ /^[^-].*[^-]$/ } @$align;            # No end gaps      @cand = grep { $_->[2] =~ /^[^-].*[^-]$/ } @$align;            # No end gaps
217      @cand = grep { $_->[2] =~ /^[^-]/ }        @$align if ! @cand; # No start gaps      @cand = grep { $_->[2] =~ /^[^-]/ }        @$align if ! @cand; # No start gaps
218        @cand = @$align if ! @cand;
219    
220      my ( $rep ) = map  { $->[0] }               # sequence entry      my ( $rep ) = map  { $->[0] }               # sequence entry
221                    sort { $b->[1] <=> $a->[1] }  # max nongaps                    sort { $b->[1] <=> $a->[1] }  # max nongaps

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