A Better Solution

A friend writing in APL found a much better solution by rearranging the data and sorting.

	A  C  T  C  G  G  positions 1 to M
	C  T  C  G  G  A  positions 2 to M+1
	T  C  G  G  A  T  positions 3 to M+2
	C  G  G  A  T  T  positions 4 to M+3
	G  G  A  T  T  C  positions 5 to M+4
	G  A  T  T  C  T  positions 6 to M+5
	 .  .  . 
	T  G  G  A  C  C 
	G  G  A  C  C  C
	 .  .  .