Hi - I made some flannel quilts a couple of years ago and had the same problem. Here is a picture of what I ended up with. I lined up the stripes up as best as I could and in the end I did lose a bit of fabric - but it's still in my stash so I'm sure I'll find a use for it some day.
Also as a hint someone suggested I use 1/2" seams instead of 1/4" because of the fraying. I'm glad I did as there was a lot of fraying.
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