What happens if you run an already soft-masked sequence on RepeatMasker again?
Do all the already soft-masked (nucleotides in small letters) get counted as repeats by the RepeatMasker and get incorporated to the overall statistics?
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biofalconch
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yh1126 •
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yh1126 •
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Since it is not mentioned in the documentation, I would assume that they will be treated the same as non masked nucleotides. But it would be great to know what happens, please do share if you try something out :)