How many calories did I really burn today during my 50 minute jog?

I use MFP to track my steps using the iPhone pedometer. I then went for a 50 minute jog at around 5mph when I enter it manually, it counts as 400 burnt calories yet my pedometer says I only burnt around 200. I'm male, 5'7", skinnyish, 145 pounds

Approximately 400 would be right. You should burn about 2.5x your body weight in calories per hour.

Figure about 100 calories a mile. You just went a little less than 5 miles so figure a little less than 500 calories.

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