INF.txt

What is the SNP? ------
What is tolerate? ------
How can we calculate # of Seed that, will be survive?
In general  
# of Seed survive = [seq length- ((#of SNP+1)(seed size))] +1        *** where seq length=100

Seed size for any SNP = seq length /(# of SNP+1) 
>	Seed size for 3 SNP =100/4=25   (in the case , at least we will find one seed Survive) see the table
Q) Suppose we have Seq length = 100 , and 3 SNP and we need size of seed equal 25 ,24, and 23 . what is the # of Seed that will be survive?
Answer)
# of Seed survive= [100 – ((3+1)(25))] +1 = [0+1]=1
# of Seed survive= [100 – ((4)(24))] +1 = [4 +1]=5
# of Seed survive= [100 – ((4)(23))] +1 = [8 +1]=9.


Seed Size--------# of Seed survive
25------|-----1
24------|-----5
23------|-----9
22------|-----13
21------|-----17

->	From where we get 9 seed ?
If we have Seq length 100, and we have 3 SNP, also we have seed size 23. then in worst case scenario we will have at least 8+1 seeds survive. (see the table) 
Why our SEED is Exhaustive?
->	If our seed size = 23 and we have 3 SNP then we will go take our worst-case scenario, which is her equal 9 seed will be survive, and compere with Seq to find the matching by using Smith waterman- and approximately we will go over all our seed to find the alignment. So, we could say it is Exhaustive.