Minimum stem length
(window)
sets the minimum stem length. This value cannot exceed either 50 or
half the sequence length.
Minimum bonds per
stem (stringency)
sets the minimum bonds per stem.
Minimum loop size
sets the minimum loop size.
Maximum loop size
(distance to furthest inverted repeat)
sets the maximum loop size (distance to furthest inverted repeat).
Sort stems by:
position
quality
size
indicates how to sort the stems in the output.
Number of stems to
show
sets the maximum number of stems to show (only applies when stems are
sorted by quality or size).
Threshold for nibbling, match
(|), and point display
The output from this program
has a '|' (vertical bar) between sequence symbols that match. This match display
character is added to the output whenever the symbol comparison
value for the two symbols in your scoring matrix is greater than or equal to
the average positive non-identical comparison value in the matrix. The Threshold for
nibbling, match (|), and point display parameter lets you specify a
match display threshold appropriate for the scoring matrix you are using.