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my @megaMotif = (
                  ["AGCT", "0", "370",  "1"],
...
                  ["TGAA", "2", "233",  "0"],
                  ["AGAG", "0", "32",   "0"]
                );

for $mega( sort{ $a->[1] <=> $b->[1] } @megaMotif )
{
        print @$mega;        
        push (@megaMot, [@$mega]);
}