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The S wave velocity structure between the hypocenter of C060394F earthquake, South Java and a series of observatory stations located in Australia and South-East Asia have been investigated through seismogram analysis in the time domain and the three Cartesian components. The synthetic seismogram is constructed from the PREMAN global earth model. Seismogram comparison between the measured and synthetic seismograms shows large discrepancies. A correction to the S wave velocity structure is needed to solve these discrepancies. Seismogram analysis and fitting at the observatory stations located in Australia show a positive anomaly, whereas the stations in South-East Asia show a strong negative anomaly. Vertical anisotropy occurred in the upper mantle layer and earth mantle layers beneath it. The seismogram analysis in the time domain and the three components simultaneously provides a better picture of the earth model, compared to the analysis of the seismogram with arrival time, travel time difference and dispersion analysis.