#Set the output files
#########################################################
#output file storing free energy table
energy = example.energy
#output file storing siRNA candidates' positions and sequences
siRNA = example.siRNA



#Folding size of the target
########################################################## 
#recommend 800 if the sequence lengh is larger than 800; 0 means whole length of target
foldsize = 0


#The following options influence the type of calculation being performed
#These are optimized for siRNA design and should only be changed for experimentation
##########################################################
#oligonucleotide's type -- r(default): RNA; d: DNA
type = r    
#Folding mode -- 
#	1: break local target structure to bind oligo; 
#	2(default): refold target RNA after oligo binding; 
#	3: no target structure considered
mode = 2	
#Folding method -- 
#	0: only consider optimal structure; 
#	1: (deprecated);
#	2(default): using partition funcion considering every possible structure  of target, can only used with mode 2; 
#	3: using suboptimal structures (suboptimal structures generared with heuristic) 
option = 2  
#start position of scanning on target
scanstart = 1 
#stop position of scanning on target (0 means scanning until the end of the sequence)
scanstop = 0  
# length of siRNA , default is 19
length = 19  
# concentration of oligonucleotide is concentration*10^unit Molar
concentration 1
unit = -7
#prefilter the unfunctional siRNA candidates
prefilter = 1
#score threshhold for prefiltering
score = 6   #cannot be re-defined yet