#An example parameter file for cases
#when overlap is allowed

#Kappa parameter for E-value calculation	
k = 0.138

#lambda parameter for E-value calculation	
lambda = 0.6	 

#Query Length
mlen = 333	

#DB Length
nlen = 7177762

#This is a protein sequence
protein

#Penalty for a gap of length 1
gap open = -12

#Additional penalty for further gap characters
gap extend = -2


Begin Alignments
Align0       5       9 38 example_align1.pir
Align1       13      8 37 example_align2.pir