Preheat oven to 375°F. Lightly coat six 2 1/2-inch muffin cups with nonstick cooking spray or line with paper bake cups and coat insides of paper cups with nonstick cooking spray; set aside.
Place raisins and water in a small microwave-safe bowl. Cook on high power for 25 seconds. Let sit for 2 minutes to plump the raisins.
In a medium bowl, stir together flours, oats, brown sugar, baking powder, and cinnamon. Make a well in the center of the flour mixture and set aside.
Combine applesauce, milk, egg whites, flax seed oil, and raisins.
Add to flour mixture; stir just until incorporated. Don’t over mix.
Spoon batter into prepared muffin cups filling each about three-fourths full.
Bake for 20 to 22 minutes or until lightly browned and the muffin is firm in the middle.
Cool in pan on a wire rack for 5 minutes. Remove from pan and serve warm.