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* The clipped out sequences are recorded in the file of '''clip_out''' | * The clipped out sequences are recorded in the file of '''clip_out''' | ||
- | * The unalignable gaps are recorded in the file of '''Gaps''', and the gaps of larger than 95th quantile (R2 are clipped. | + | * The unalignable gaps are recorded in the file of '''Gaps''', and the gaps of larger than 95th quantile (R2_gap=0.95) are clipped. |