We present an analysis of the substructure revealed by 407 RR Lyraes in Sloan Digital Sky Survey (SDSS) Stripe 82. Period estimates are determined to high accuracy using a string-length method. A subset of 178 RR Lyraes with spectrally derived metallicities are employed to derive metallicity-period-amplitude relations, which are then used to find metallicities and distances for the entire sample. The RR Lyraes lie between 5 and 115 kpc from the Galactic center. They are divided into subsets of 316 RRab types and 91 RRc types based on their period, colour and metallicity. The density distribution is not smooth, but dominated by clumps and substructure. Samples of 55 and 237 RR Lyraes associated with the Sagittarius Stream and the Hercules-Aquila Cloud respectively are identified. Hence, ~ 70 % of the RR Lyraes in Stripe 82 belong to known substructure. There is a sharp break in the density distribution at Galactocentric radii of 40 kpc, reflecting the fact that the dominant substructure in Stripe 82 - the Hercules-Aquila Cloud and the Sagittarius Stream - lies within 40 kpc. In fact, almost 60 % of all the RR Lyraes in Stripe 82 are associated with the Hercules-Aquila Cloud alone, which emphasises its pre-eminence. Additionally, evidence of a new and distant substructure - the Pisces Overdensity - is found, consisting of 28 faint RR Lyraes centered on Galactic coordinates (80 deg, -55 deg) and with distances of ~ 80 kpc. The total stellar mass in the Pisces Overdensity is ~10000 solar masses and its metallicity is [Fe/H] ~ -1.5.
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