We present the results of $^{12}$CO($J$=1-0) mosaicing observations of the cD galaxy NGC 1316 at kpc-resolution performed with the Morita Array of the Atacama Large Millimeter/submillimeter Array (ALMA). We reveal the detailed distribution of the molecular gas in the central region for the first time: a shell structure in the northwest, a barely resolved blob in the southeast of the center and some clumps between them. The total molecular gas mass obtained with a standard Milky-Way CO-to-H$_2$ conversion factor is $(5.62 pm 0.53)times10^8$ M$_odot$, which is consistent with previous studies. The disturbed velocity field of the molecular gas suggests that the molecular gas is injected very recently ($<1$ Gyr) if it has an external origin and is in the process of settling into a rotating disk. Assuming that a low-mass gas-rich galaxy has accreted, the gas-to-dust ratio and H$_2$-to-HI ratio are unusually low ($sim 28$) and high ($sim 5.6$), respectively. To explain these ratios, additional processes should be taken into accounts such as an effective dust formation and conversion from atomic to molecular gas during the interaction. We also discuss the interaction between the nuclear jet and the molecular gas.
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