Parking is free for motorcyclists in the city of Toronto only when it is legal to park. Parking your bike in a location that prohibits parking will still result in tickets. For example, If you park your bike in a fire route, you will still get a ticket. Likewise, you can still get a ticket if you park your bike in a 'no parking' zone, or, in your case, parking in a 'conditional parking' zone outside the permitted times.
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