The trough appears to be an aulacogen, a failed arm of a triple junction of a plate tectonics rift system, formed during the initial stretching phase when Gondwana was breaking up. The rift was formed by the same forces that created the rift system in South Sudan, and connects those rifts to the Lamu embayment further to the south. The separation of the other two arms of the junction allowed India-Madagascar to separate from Africa. The trough is now hidden by a cover of Quaternary sediments and volcanic rocks.
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