Get a metronome. Set it to something pretty easy... like 60 bpm (or less if you're not comfortable). I suggest trying it out at 60 bpm if that's too fast just back it off. Play the tab that I provide at bottom, hitting the first note of each four note(notes in parenthisis) group on beat. Tapping your foot is a good way to stay in time. Also another way to keep yourself in time is to emphasize every bold note as well... simply do this by striking it a bit harder. You can run through this fairly slow with simple downstrokes then run through it with alternate picking. You can also use this anywhere on the fretboard, not just where I show you. Just take the pattern and translate it where you want to start. I always start on the 5th fret on the lowE string then move my way down the fingerboard.

e|-----------------------------------------------------------------------
B|-------------------------------------------------------------(7)-8-9-10
G|------------------------------(5)-6-7-8-(9)-8-7-6-(7)-8-9-10----------
D|---------------------(5)-6-7-8-----------------------------------------
A|-----------(5)-6-7-8---------------------------------------------------
E|-(5)-6-7-8-------------------------------------------------------------

e|-(7)-8-9-10-(11)-10-9-8-----------------------------------
B|------------------------(11)-10-9-8------------------------
G|------------------------------------(11)-10-9-8------------
D|-----------------------------------------------(11)-10-9-8-
A|-----------------------------------------------------------
E|------------------------------------------------------------

e|-----------------------------------------------------
B|-----------------------------------------------------
G|-----------------------------------------------------
D|-(7)-8-9-10-(9)-8-7-6-------------------------------
A|----------------------(9)-8-7-6----------------------
E|--------------------------------(9)-8-7-6-(5)--------

Notice how you end on the same note that you started on... Next you slide to the 6th fret on the lowE string and use it as your starting note and use this same pattern... Then go to the 7th and so on. Once you get comfortable with the pattern at your starting tempo... bump it up about 5 bpm and try it. Keep going until you can't do it accurately anymore. Then back it up a few bpm and practice at that speed for a few minutes.

NOTE: this exercise was taken from a John Petrucci film. I'm not certain if it's exactly like his or not... but it's close. I haven't seen the video in forever. I've been using this for about 2 years now though.