RNA Folding Form for 3.236.47.240

RNA Folding form for 3.236.47.240

The folding temperature is fixed at 37°. You may still fold with the older version 2.3 RNA parameters, which allow the temperature to be varied.

Enter sequence name:    

Enter the sequence to be folded in the box below. All non-alphabet characters will be removed.
FASTA format may be used. The current limit is 2400 nucleotides.



   

Enter constraint information in the box at the right. (optional) You may:


  1. force bases i,i+1,...,i+k-1 to be double stranded by entering:
    F   i   0   k on 1 line in the constraint box.
  2. force consecutive base pairs i.j,i+1.j-1, ...,i+k-1.j-k+1 by entering:
    F   i   j   k on 1 line in the constraint box.
  3. force bases i,i+1,...,i+k-1 to be single stranded by entering:
    P   i   0   k on 1 line in the constraint box.
  4. prohibit the consecutive base pairs i.j,i+1.j-1, ...,i+k-1.j-k+1 by entering:
    P   i   j   k on 1 line in the constraint box.
  5. prohibit bases i to j from pairing with bases k to l by entering:
    P   i-j   k-l on 1 line in the constraint box.
  • The RNA sequence is
  • Folding temperature is fixed at 37°.
  • Ionic conditions: 1M NaCl, no divalent ions.
  • Enter the percent suboptimality number.
  • Enter an upper bound on the number of computed foldings.
  • Enter the window parameter if you wish.
  • Enter the maximum interior/bulge loop size
  • Enter the maximum asymmetry of an interior/bulge loop
  • Enter the maximum distance between paired bases if you wish.
  • Choose image width for png & jpg files: Small: Regular: Medium: Large: XLarge: Huge:
  • Choose structure format: Automatic: Bases: Outline:
  • Grid lines in energy dot plot On: Off:
  • Choose structure draw mode:
  • Choose exterior loop type:
  • Choose base numbering frequency:
  • Choose sequence numbering offset:
  • Choose regularization angle in degrees: (Not used if 0.)
  • Choose structure rotation angle:
  • Choose structure annotation: None: p-num: ss-count: high-light:

    Enter high-light regions(s):