Although the mechanical response of DNA to physiological torsion and tension is well characterized, the detailed structures are not yet known. By using molecular dynamics simulations on linear DNA with 300 base-pairs, we provide, for the first time, the conformational phase diagram at atomic resolution. Our simulations also reveal the dynamics and diffusion of supercoils. We observe a new state in negative supercoiling, where denaturation bubbles form in adenine/thymine-rich regions independently of the underlying DNA topology. We thus propose sequence-dependent bubbles could position plectonemes in longer DNA.