If you were unable to remove the roof stains with the bleach solutions it may be time to seek a professional. There are some roof stain removal steps that tell you to use a Lye-based solution, but this can cause serious damage to the shingles if done the wrong way.
Tips for Roof Stain Prevention
There are a few ways to prevent the mold and mildew that stain your roof. To apply the chemicals to your roof can be tricky and you will need to choose the right product for the type of shingles you have on your house. For this reason you will want to talk to a professional and have them put the products on the roof.
If you are in the market for a new roof it might be a great idea to spring for the resistant shingles. They do cost a little more, but they will save you time and money in the end. These are not that popular as of yet, meaning they might be harder to find than the other more traditional shingles.