Annotation of the folded sequence with constraint information.

When constraints are used, the displayed sequence on the main output page is annotated to indicate what constraints were used.

1. F i 0 k: Bases i, i+1, ... i+k-1 are underlined by the letter F (force). This indicates that these bases must pair.
2. F i j k: Base pairs i.j, i+1,j-1, ..., i+k-1.j-k+1 are forced. This is indicated by placing a "(" under the bases i, i+1, ..., i+k-1 and a ")" under the bases j, j-1, ..., j-k+1. Note that the forced base pairs are uniquely determined by this bracket notation because pseudoknots are not allowed in computed foldings. Any impossible base pairs (non-canonical) will be designated by a pair of "!"s. The same is true in 4. below.
3. P i 0 k: Bases i, i+1, ... i+k-1 are underlined by the letter P (prohibit). This indicates that these bases must remain single stranded in any folding.
4. P i j k: Base pairs i.j, i+1,j-1, ..., i+k-1.j-k+1 are prohibited. This is indicated by placing a "{" under the bases i, i+1, ..., i+k-1 and a "}" under the bases j, j-1, ..., j-k+1. The prohibited base pairs are not uniquely determined by this bracket notation, but this should not cause any confusion. In the example below:

            10         20         30         40         50         60
    CGCGCGCGCG AAAAACGCGC GCGCGAAAAA CGCGCGCGCG AAAAACGCGC GCGCG
    {{{{{{{{{{      {{{{{ {{{{{      }}}}}}}}}}      }}}}} }}}}}
        A                B                C               D
   

   it is not clear from the annotated sequence whether the helices A-C and B-D were prohibited, or the whether A-D and B-C were prevented. If these helices were being forced, the interpretation would be unambiguous, since forcing A-C and B-D would create a pseudoknot, which is forbidden.
5. P i j k l: The segment i, i+1, ..., j is not allowed to form any base pair with the segment k, k+1, ..., l. This is indicated by underlining the 5' segment, i, i+1, ..., j by a lowercase letter, and the 3' segment, k, k+1, ..., l by the same uppercase letter. Different letters are used for different pairs of segments, and F & P are avoided.