First you need to parse your file. What have you already tried? Can we see your code?

(When you post your code, please remember to read the Writeup Formatting Tips.)

now i want to make each line as an array and give the first one as the name of the
like this
@IL12::1::287 = ('6','-17','-9','-21','-24','-15','-2','11','4','4','-15','-26','-16','-9','-18','-25','27','17','6')

Please don't use variables as variable names (yes this still applies).

Second, you'd do better to store your arrays as references in a hash, where the keys to the hash could be 'IL12::1::287', 'IL12::1::329', etc.
(Update: thezip gives you an example of the data-structure below.)

As for the array "common elements" problem, the usual way to solve that is to build a hash containing the elements of the first array as keys, then to loop through the elements of the second array testing for existence in the hash.

  # you have @arr1 and @arr2
  my %lookup = map { $_ => undef } @arr1;
  my @common = grep { exists $lookup{$_} } @arr2;
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-David