I think you better parse file2 and file3 into hash of arrays. Something like:

my $file2 = {

    string11 => [ "AGCTAGCTG", "CAGAGTC" ],
    string123 => [ "AGCTGAAGA" ],
    string12 => [ "AGCGATTATCGA", "AGCATGAAGACC", "ACAGCATGACTA" ],
......
};
[download]

And same for file3. After that you can easly manipulate your data.