if(($sequence=~/ABC/)  ?????
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I guess two (( is a typing mistake. but that implies this is not copy-past of your code....

$sequence= "ABC";
open (OUT, ">OUTFILE");
if($sequence=~/ABC/)        
{
       
    print OUT "blas\n";
}
close (OUT);
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this works, so the error must be somewhere else. are you sure you are getting inside the if block ?