1. Divide the given chromosomal region into M sliding windows with K variants per window and a sliding step of K/2

2. for each sliding window wl do

3. estimate $\frac{1}{\overline{d_l}}$ and $\frac{ln2}{{\stackrel{\sim }{d}}_l}$

4. if $\left(\frac{1}{{\overline{d}}_l}<=\frac{ln2}{{\stackrel{\sim }{d}}_l}\right)$ do

5. return(NULL)

6. end if

7. else do

8. define index t←0

9. while $\left(\frac{1}{{\overline{d}}_l}>\frac{ln2}{{\stackrel{\sim }{d}}_l}\right)$ do

10. sort distances dl in an decreasing order

11. remove dl [t]

12. determine the chromosomal position of the removed gap: p[dl [t]]

13. t← t + 1

14. end while

15. return {p[dl[t]]}

16. end else

17. end for

18. sort {p[dl[t]]} in an increasing order and group variants according to spatial breaks