If I am understanding your question, you might do something likesomething like:

open FILE "<file1.text" or die "can't open file1 $!";
close FILE;
while( <FILE> ){ $blurb{$_}++ if /^Query\b/ }
open FILE "<file2.text" or die "can't open file2 $!";
while( <FILE> ){ print if /^Query\b/ && $blurb{$_}; }
close FILE;
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