ss-count is the propensity of a base to be single
stranded, as measured by the number of times it is single stranded in
a group of predicted foldings. The ss-count file gives the
number of predicted foldings on the first line. The ith
subsequent line contains i and the number of foldings in which the
ith base was single stranded. The plotting option gives
plots of ss-count values averaged over a user selected window.
Maximium size of a bulge/interior loop
The upper bound on the total number of single-stranded bases
that are allowed in a bulge or interior loop. The default value is 30. The user may
select any smaller value.
Maximum asymmetry of a bulge/interior loop
The upper bound on the asymmetry of a bulge/interior
loop. This parameter is the maximum size of a bulge loop. For interior
loops, if the number of single-stranded bases on the two sides are
n1 and n2, then |n1 - n2|
<= this limit.
Sequence numbering offset
This number will be added to the base labels. If you wish, for
example, your sequence to begin with base N, then set OFFSET to
N-1. The default is 0, or no offset.