The only differences are the price and the restrictions (advance purchase, ability to change, etc.) They're the same seats with the same service (or lack of service, as the case may be).
Airlines often have several different economy fares per flight. The letters are used to keep track of the inventory. For example, let's take a hypothetical flight that has 100 seats on the airplane. The round trip fares are $250, $400, $600, and $1,000. Each will be assigned a different letter.
The $250 seats (let's call them "Q") will have the most restrictions and the fewest number of seats available. Once they sell out, you have to buy a more expensive seat. The $400 seats (let's call them "V") may have fewer restrictions and will also have a limited number of seats. Again, you have to buy a more expensive seat once they sell out. The most expensive fare (called "Y" on most airlines) will have no restrictions and is available for every economy class seat on the flight.
The system is confusing and frustrating to travelings. However, it helps airlines manage revenue. They don't want to fly with empty seats, so they stimulate demand by offering some discounts. However, they don't want to sell every seat at the cheapest price or they won't be able to make any money.
Different airlines may use different letters for the same fare, but they all basically work in this manner.
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