I'm confused about the startup disks

When I press 'option (alt)' when booting up, the mac takes me to a screen with three startup disks I can choose from, those being:
1. Macintosh HD (which is the default and only one I use)
2. Recovery 10.9
3. Windows
What are #2 and #3 for?
I think #2 is a tool that comes preinstalled?
Regarding #3, I've installed Windows 7 via bootcamp on my mac before but it wasn't as convenient as i expected so I deleted it via bootcamp again. Now I cannot find any traces of Windows 7 using either bootcamp or disk utility, so why is the windows partition still there?
*My usb on the right side of the mac just stopped working as intended and instead cannot detect whatever I plug in (mouse, hard disk etc...) after I installed Windows 7 and I still have that problem now even thought I've already deleted the Windows partition. So I thought that this startup disk thing might be the problem.
Early 2013 Retina 15-inch macbook pro running mavericks OSX.
Would be so grateful for any any answers!
Thanks in advance,
pip_wu

Number 2 is the Recovery partition you boot from to do maintenance on the system drive, such as repairing the disk with Disk Utility or reinstalling an operating system.  Hopefully you will never need to use it but it is there when you need it.
Number 3 appears to be the partition you created for Windows.  Deleting Windows from that partition does not remove the partition.  It may be an empty partition at this time.
For the USB problem, try an SMC reset.
http://support.apple.com/kb/HT3964

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