Compare 1.4 million sites against 1 million authoritative sites

I have a list of about 1.4 million URLs (Sites A) that need to be checked against another 1 millions sites (Sites B). Sites B are the authoritative sites that are from Alexa’s top 1 million sites. I would like to have a program or script made that each of Sites A (1.4 million URLs) checked if it is listed in Sites B in a reasonable time (say, in less than 1 hour, but faster the better). The program can be made with: C, Ruby, Perl, or Python etc. When the URL of one site in Sites A is listed in Sites B, I will need a flag be put up, and it must be saved as a text file along with the URL, one site per line. When the site in Sites A is not listed in Sites B, it will have a flag put down and it also be saved as a text file along with the URL.