For a decent estimate, figure out the total number of minutes you spent walking and the total amount you spent running, and multiply each by the appropriate number of Calories/minute (Here is a site with some speed vs. energy expenditure charts). If you don't know how fast you run/walk find a measured track (they're usually 200 or 400m) and time yourself. Many smartphones have good enough GPS to give you your running speed too.
This calculation is a little bit of an oversimplification since your energy expenditure will remain elevated throughout the walking interval. If you're willing to put a bit of money into it, get a GPS/heart rate monitor. The good ones combine a number of factors to estimate your caloric expenditure. I have an older one, and although the GPS can't handle being under any tree cover whatsoever, it's an awesome training tool for running on the road.
I think this next bit is negligible, but for completeness: even using a GPS/heart rate monitor wont factor in the calories you burn due to an elevated metabolism after exercising. This study compared the calories burned after running continuously or with high-intensity (anaerobic) intervals. The people who did the high-intensity intervals burned about twice as many extra calories in the nine hours post-exercise: 64 vs. 32 additional Calories. Since the subjects were all 21-year-old males, these numbers probably aren't generalizable to the general population, but they at least give you a ballpark idea.
