Indonesia is a maritime continent country that lies between the Indian Ocean and the Pacific Ocean. Therefore, the interaction between ocean and atmosphere plays an important role in the formation of weather and climate phenomena. A good understanding of ocean-atmosphere parameters on the scale of intra-seasonal is needed accordingly to the WMO (World Meteorological Organization) program on Sub-Seasonal to Seasonal Project. This study will discuss the Sea Surface Temperature (SST), meridional wind and precipitation to identify the strength of the relationship, to analyze the variations and to obtain cycle/periodicity in the maximum periods of one hundred days. Those data were from NOAA and TRMM satellites for the years of 2002-2015, processed and analyzed using correlation, spatially and temporally. Data were transformed using Fast Fourier Transform and spectral analysis which performed using periodogram of Power Spectral Density. The result showed that the Flores Sea, Banda Sea and Arafura Sea have the strongest relationship on the precipitation with SST and meridional wind. These waters also have the lowest value on the SST and rainfall, and relatively more predictable due to small different from the value of day n-1. Compared to Australian Monsoon, Halmahera Sea has a higher rainfall because it is more influenced by the flow of warm sea currents from warm pool in the north Papua. Meridional wind in the waters of western Indonesia is influenced by the Madden Julian Oscillation. The periodicity strength of SST, meridional wind and rainfall in western and eastern Indonesia waters are not always comparable because there is a time lag.
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