I have a 2000 Honda rebel and the engine will not turn over. I stored it over the winter but I put new gas in it and I have rode it twice already this year. I has sat a couple of weeks and now the engine wont turn over and after a few tries the battery will spark. I'm not thinking the battery is bad because all the lights and everything else seems fine. I thinking there is a short somewhere. I also cleaned the battery.

The first thing you want to do is check the oil. Drain and refill. If you see metal filings you have a problem if you don't you have just caught up on maintenance you had to do anyway.
If this model has a radiator check for coolant. I doubt it seized while sitting there but you will want to know. Make sure the level is up to where it's called out in the service manual.
Can you manually kick the engine over with the kick starter. If not take the spark plug/plugs out and try rotating the engine by rolling it back and forth while in gear. If it's seized up it will just skid the rear time. Replace the plugs and try to start again if engine turns. You've pretty much isolated the starter.
If this is an electric start only model (No Kick Starter) you should be able to push start its and charge the battery while running.
Check the connections to the starter and retry. You may have to change out the starter if it won't crank.
Best regards,
TF