Some suggestions:
That's a bit awkward, because you call read_file_line() inside and outside your while loop, so maintenance-wise it would be easy to change one and forget to change the other. You could combine both calls into your while loop condition:

while(my $pair1 = read_file_line($f1) and my $pair2 = read_file_line($
+f2)){
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Also, since you only use $value inside the loop, there's no need to declare it outside. Just declare it with my when you assign to it inside the loop. Declaring it outside the loop means it'll retain its value between loops, which shouldn't hurt in this case, but can make odd things happen if the assignment to it is ever conditional.

In your print statement, there's no need to concatenate all those things. Just put your variables and \t characters inside one set of quotes.