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According to Us Weekly, the singer-songwriter's new single "Shadow Days" (from the album Born and Raised, available May 22) is actually about Aniston, whom he dated more than three years ago.
"'Shadow Days' is about Jen," a source tells Us. "It really took him a long time to get over her. He really loved her a lot."
Mayer (whose famous exes include Jessica Simpson, Taylor Swift and Jennifer Love Hewitt) sings in the song: "You find yourself alone... I found myself in pieces/ On my hotel floor/Hard times help me see/I'm a good man with a good heart/Had a tough time, got a rough start/And I finally learned to let it go."
The source explains the lyrics: "He wrote the song as a farewell letter knowing [Jen] would hear it. Ultimately he's done a lot of self reflection though, and he realizes they weren't right for each other."
The musician, 34, and the Wanderlust star, 43, started seeing each other in April 2008 and dated on and off until late 2009. Aniston has been with her Wanderlust costar Justin Theroux for more than a year.
"[John and Jen] weren't right for each other, but he is really a good guy," she source adds.