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 #!/usr/bin/perl -w
use strict;
use warnings;     
...
    if($line =~ m/^\>/){my $name=$line;$name =~ s/(F29-2,F29-3,F29-4,F
+44-2,F53-2,F38-3,F12-2)/$replace{$1}/;print $name;}   
    elsif ($line!~m/^\>/){print $line;}
  }