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Hatha yoga disciplines involve seated poses as well as standing poses, and many classes will involve some time spent in one of several seated positions, usually a seated cross-legged pose (sukhasana) or thunderbolt pose (vajrasana) in which you kneel on the floor and sit back on your heels. In some Hatha yoga classes you will simply sit in these positions, or they may be used as preparation for other poses.
If your knees are higher than your hips when you sit cross-legged, it means that you have tight hips, which is especially common in runners. Try sitting on a block or blanket to help your hips open. Believe it or not, simply sitting in a cross-legged position will increase the flexibility in your hips.
Similarly, if you have tight hips and thighs it may be too uncomfortable for you to sit back on your heels in thunderbolt pose. If so, place a rolled blanket between your thighs and calves. Some people with tight ankles experience ankle discomfort in thunderbolt pose. If you are one of these people, place a rolled blanket or towel between your ankles and the floor to relieve the pressure on the tops of your ankles.