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6.1.1 Traceback errors

Errors in the traceback subroutine that computes structures from the energy matrices are indicated by messages such as ``Open bifurcation not found between ??? and ???'', ``Bulge or interior loop closed by ???, ??? not found'' and ``Closed bifurcation not found between ??? and ???''. These messages are useful debugging tools when changes are being made in the program, but they should not occur during normal use. If such a message occurs, check that the sequence being folded is a legitimate nucleic acid sequence in uppercase letters. Trying to fold a sequence that has no secondary structure will generate an error message of this type.

Michael Zuker
Thu Nov 2 14:28:14 CST 1995