adder - 1:22 pm on Aug 31, 2013 (gmt 0)
Majestic SEO - but it won't work with your data. It only works from its own database (which should have the majority of your links indexed anyway).
Or alternatively, if you insist working with your own list, post a job on oDesk and get somebody to write you a script. If I understand you correctly, this is a very simple job for somebody who knows PHP and Regular Expressions.