How does one get identified through Tor?
Tor is a web browser, that attempts to ensure anonymity by routing web traffic through a series of Tor nodes. Each node only knows which node it is receiving the packet from, and which it is delivering to. The nodes used change every few seconds. The overall internet system used by Tor is called the onion network.
There are several ways in which one gets identified even though using Tor.
The most important with regards to overall security and privacy is that if someone has access to entry and exit nodes, using a bit of intelligence, it is possible to start recognizing a pattern. Given that the US Government does own some entry and exit nodes, it only makes sense they are putting the pieces together.
The second most important method of being identified is through your browser fingerprint. Although you may think your computer is pretty much just like most others out there, there are indeed unique qualities about your computer that can identify it. Once identified, it can be tracked across the web.
The good news is that this part of the puzzle is easy to work around (although few do). That is to have a computer that is EXACTLY, PRECISELY stock. No added anything. Even better is to create a bootable Tails thumb drive (perform a web search on Tails). This is a bootable system with all the tools you need (browser, email, etc.) and since every user of Tails looks the same, makes you able to hide in plain sight.