I see this a lot on cars, especially those that sit outside like yours, near or under trees / bushes or where water comes off roofs onto the car.
In a way its akin to mildew, where the spores collect and grow along your cars window seal line.
You also see it on top of caravans.
Put the windows fully down and check the soft black brush / felt material that acts as the window protector - has it got the green mould on it?
If yes you are going to have to get rid of this too. Try a strong solution of all general purpose cleaner, say G101 or similar, get a small brush in there and remove all green traces.
For rubber protection I like Aerospace 303, if need be apply after every wash.
Have a look on the Cleanyourcar web site, there should be loads of products on there.
Only other alternative is an outdoor car cover just for the roof?