My right knee is not aligned with my foot when i put my foot straight my knee looks crooked and little painful when i run its worse what's wrong?

Don't run!: Always move away from pain, don't go into pain. It sounds like there's a misalignment going on between your hip, knee and foot. So you could benefit from getting a second opinion from a osteopathic physician (DO), who can evaluate your musculoskeletally, and also treat you. If this doesn't work s/he can refer you to PT, or in more serious cases, to orthopedics. Please make an appointment soon, so you can go back to your active lifestyle.