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The code will probably include an URL that looks like this:
http://www.youtube.com/v/FI76sKLMkMU&color1=0x006699&color2=0x54abd6
You can change the two colors from the URL (color1 and color2) to any value you want: the 216 web safe colors are a good start, but don't forget to replace "#" with "0x".
Here's a list of other YouTube parameters that could be useful if you want to manually edit the code (the default values are in bold):
* border (values: 0, 1) - if the value is 1, shows a border around the video
* rel (values: 0, 1) - if the value is 0, the player doesn't show related videos
* autoplay (values: 0, 1) - if the value is 1, the video starts to play automatically
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