This is quite a common problem but it is hard to say what is causing it. Sometimes it is "dead pixels" like what you got on a tv screen if you leave it paused on a channel for hours. OR it could be the processor trying to keep up with you. If you can afford to - try and restore the device and see if the line is still there and let me know.
For more guides, videos and tips on how to use the iPad visit :
http://www.tabletmastered.com/blog/
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