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The convolutive blind source separation (BSS) problem can be solved efficiently in the frequency domain, where instantaneous BSS is performed separately in each frequency bin. However, the permutation ambiguity in each frequency bin should be resolved so that the separated frequency components from the same source are grouped together. To solve the permutation problem, this paper presents a new alignment method based on an inter-frequency dependence measure: the powers of separated signals. Bin-wise permutation alignment is applied first across all frequency bins, using the correlation of separated signal powers; then the full frequency band is partitioned into small regions based on the bin-wise permutation alignment result. Finally, region-wise permutation alignment is performed in a region-growing manner. The region-wise permutation correction scheme minimizes the spreading of the misalignment at isolated frequency bins to others, hence to improve permutation alignment. Experiment results in simulated and real environments verify the effectiveness of the proposed method. Analysis demonstrates that the proposed frequency-domain BSS method is computationally efficient.