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Secondary structure map
We transcribed the secondary structure mapping using the arb-compatible SILVA and greengenes databases. The files contain one column. Each row in the column indicates the row that row maps to. If there is a 0 in the row, then that position is in a loop. There needs to be an equal number of rows and bases in the alignment. For example, the SILVA secondary structure map file contains 50,000 rows. You are free to construct your own secondary structure mapping files.