The number after the notes indicates the octave so we can see that there's a 2 octave difference between the two E on the 6th and 1st strings. You can listen to the sound of the individual tuned strings in the midi file below:
If you bought a Guitar Tuner along with your guitar, now it's the time to turn it on and watch the all the arrows and dials move while you gently turn the tuning pegs till your guitar is perfectly tuned.
If you didn't buy one you have two options: 1) go and buy one now 2) keep on reading.
You will need a reference tone, it could be a keyboard, a tuning fork or the midi file on this page. Play the 6th string and slowly turn the peg until the note you play matches the reference E tone. It's usually best to tune up to the note raher than down: if the note on the guitar is sharp (higher than the reference tone), turn down the peg until it's slightly flat (lower than reference) and then slowly raise it until it's exactly in tune.
If the strings are new or the guitar is really out of tune, you may want to give the string a tug by pinching it between your thumb and forefinger and pulling it up about a half inch from the fretboard. This helps the string settle on the tuning peg and stabilize the tuning especially on acoustics and non-locking tremolos.
Once the 6th string is tuned play the note on the fifth fret. As you can see in the tab below, it is an A, the same note as the open (not fretted) 5th string. Use this note as a reference to tune the fifth string.
Once the fifth is in tune, play it at the fifth fret (D) and tune the fourth string and repeat the process with the remaining strings, remembering that on the 3rd string you'll have to play a B on the fourth fret to tune the second string.
If you have a tuning fork (which is usually tuned to an A) you must begin tuning from the fifth string.
Now your guitar should be in tune and ready to be played.