It takes about a week after pregnancy to be able to identify if you're pregnant or not. In this case the egg in your ovaries would already be infertile by this stage of the cycle. Also, being 16 you're still hormonal and your cycle isn't always every month on the same day. I've completely missed cycles of my period and have not got pregnant. I am safe to assume you're not. Especially if you've been using birth control methods some of these, such as the Depo Povera, can alter your cycle slightly, or majorly, depending on severity, and your dates of your menstural cycle could be different.
However, if you're still not sure go see your GP and talk to them.
If I understand you, you are thinking you are pregnant because your period arrived three days late? I think given the fact that you had sex so late in your cycle, and then your period did arrive, you shouldn't be that worried about being pregnant. If you like, have a home pregnancy test on about the 15th, to confirm the negative, but you are probably OK.