I mainly ride and find running much harder work than cycling, I usually experience what you describe if I set off far too fast. Fast for me is doing the first mile in about 8:30 minutes (not fast for many but fast for me), if I get carried away and allow that to happen then the latter parts of the run really hurt.
I also found that when I increased my longest run to 7 or 8 miles then on the shorter runs I started to naturally increase my pace a little and they felt easier. In the summer when I was only doing a couple of 4 mile runs a week it never felt like it was getting any easier. Increasing the length of one of your runs gradually (run as slow as you like) will help your running fitness. I'm running three times a week at the minute as I am training for a couple of races and the extra run also has helped, in the summer I drop it back.



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