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revision 1.3, Sat Aug 21 17:43:32 2010 UTC revision 1.4, Mon Nov 8 19:49:39 2010 UTC
# Line 292  Line 292 
292      my @cand;      my @cand;
293      @cand = grep { $_->[2] =~ /^[^-].*[^-]$/ } @$align;            # No end gaps      @cand = grep { $_->[2] =~ /^[^-].*[^-]$/ } @$align;            # No end gaps
294      @cand = grep { $_->[2] =~ /^[^-]/ }        @$align if ! @cand; # No start gaps      @cand = grep { $_->[2] =~ /^[^-]/ }        @$align if ! @cand; # No start gaps
295        @cand = @$align if ! @cand;
296    
297      my ( $rep ) = map  { $_->[0] }                     # sequence entry      my ( $rep ) = map  { $_->[0] }                     # sequence entry
298                    sort { $b->[1] <=> $a->[1] }         # max nongaps                    sort { $b->[1] <=> $a->[1] }         # max nongaps

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