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The energy efficiency of a home relies on several factors.
The most dominant of these factors is the insulation used, both within the perimeter walls and attic. This would include the houses ability to breath as well as maintain a good barrier. It's not so much the amount of insulation as the type and installation methods.
Another factor that effects the energy efficiency of your home is your windows and doors. They come in all varieties of energy ratings, and are also reliant on the installation methods used.
The third thing that I would look at is the ventilation of your attic. If your attic has the necessary ventilation needed it can reduce energy cost as well as prolong the life of your roof system.
Using the information you have provided and not visually inspecting the roof, the black spots on your roof are more than likely algae. Most shingle manufacturers use copper or zinc coated granules to aid against the growth of algae. As the rain washes over your shingles, particles of the copper are dispersed helping the prevention of algae growth. Most manufacturers warranties will cover the first 10 years against streaking and staining, which helps to explain why you have not seen evidence of this issue before. There are low pressure solutions available to clean your roof but they will not prevent the stains from returning. The addition of copper or zinc strips under the first full course of shingles below the ridge cap could provide to be a longer lasting remedy. I suggest that you contact a reputable local roofing contractor for a complete roof inspection before you make a decision on the remedy, as the algae can hold moisture and can prematurely age your shingles. ( Damon Ward Project manager At Allstate Exteriors llc.)
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