Black Spots on my Chestnut

Need advice on how to remove black spots on my wood and canvas Chestnut. I store the canoe outside in the summer, covered by a Bag Lady cover (not waterproof). In the winter I store it in the garage (unheated). After the removing the canoe cover last summer I noticed small black spots on the red paint. I tried to remove the spots with soapy water. Then I tried mold remover spray. Nothing worked. The spots appear to be located on the canvas, beneath the outside red paint.
I assume the black spots are a result of using a tight cover all summer-the cover got wet and the canoe was not able to "breath" and dry out. Mold developed.
Any suggestions on how to remove the mold, short of recanvassing the canoe? Thanks for your help!
 
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