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SN~1993J in M81 was the brightest supernova in the northern hemisphere since SN~1954A in NGC~4214. As such it provided a great opportunity to study the details of supernova line emission over a fairly long period of time. Here we present an analysis of the emission line structure at moderate velocity resolution of SN~1993J over the course of a year from the onset of the nebular phase. Only SN~1987A has been observed for more of its evolution and with such detail. Several of the emission lines, notably [O~I] $\lambda$5577, [O~I] $\lambda\lambda$6300, 6364, O~I $\lambda$7774, and Mg I] $\lambda$4571, show small scale variations that indicate inhomogeneities in the ejecta. These clumps in the ejecta are long-lived, with the patterns of variation in the velocity structure of the lines remaining consistent over time scales of months. The patterns are also consistent within a given species, for both forbidden and permitted transitions. [O~I] $\lambda$6300 and [O~I] $\lambda$5577 show the same clumping signature as O~I $\lambda$7774. The clumping follows different patterns for other species, with Mg I] $\lambda$4571 having a different velocity structure than any of the oxygen lines. This may show that the magnesium and oxygen emission originate in different clumps within the ejecta. In contrast to these emission lines, [Ca~II] $\lambda\lambda$7291, 7323 show little evidence for inhomogeneities, perhaps indicating emission from the general stellar envelope, rather than clumps ejected from the stellar core. H$\alpha$~ also shows a complicated velocity structure differing from the other lines, but this is not evident until late times. It seems unrelated to the long-lived patterns due to clumps and is more likely due to Rayleigh-Taylor instabilities between the forward and the reverse shocks.
