Not So Naive example

First attempt
G	C	A	T	C	G	C	A	G	A	G	A	G	T	A	T	A	C	A	G	T	A	C	G
	1	2	3
G	C	A	G	A	G	A	G

Shift by: 2 (l)

Second attempt
G	C	A	T	C	G	C	A	G	A	G	A	G	T	A	T	A	C	A	G	T	A	C	G
			1
		G	C	A	G	A	G	A	G

Shift by: 1 (k)

Third attempt
G	C	A	T	C	G	C	A	G	A	G	A	G	T	A	T	A	C	A	G	T	A	C	G
				1	2
			G	C	A	G	A	G	A	G

Shift by: 2 (l)

Fourth attempt
G	C	A	T	C	G	C	A	G	A	G	A	G	T	A	T	A	C	A	G	T	A	C	G
					8	1	2	3	4	5	6	7
					G	C	A	G	A	G	A	G

Shift by: 2 (l)

Fifth attempt
G	C	A	T	C	G	C	A	G	A	G	A	G	T	A	T	A	C	A	G	T	A	C	G
								1
							G	C	A	G	A	G	A	G

Shift by: 1 (k)

Sixth attempt
G	C	A	T	C	G	C	A	G	A	G	A	G	T	A	T	A	C	A	G	T	A	C	G
									1
								G	C	A	G	A	G	A	G

Shift by: 1 (k)

Seventh attempt
G	C	A	T	C	G	C	A	G	A	G	A	G	T	A	T	A	C	A	G	T	A	C	G
										1
									G	C	A	G	A	G	A	G

Shift by: 1 (k)

Eighth attempt
G	C	A	T	C	G	C	A	G	A	G	A	G	T	A	T	A	C	A	G	T	A	C	G
											1
										G	C	A	G	A	G	A	G

Shift by: 1 (k)

Ninth attempt
G	C	A	T	C	G	C	A	G	A	G	A	G	T	A	T	A	C	A	G	T	A	C	G
												1
											G	C	A	G	A	G	A	G

Shift by: 1 (k)

Tenth attempt
G	C	A	T	C	G	C	A	G	A	G	A	G	T	A	T	A	C	A	G	T	A	C	G
													1
												G	C	A	G	A	G	A	G

Shift by: 1 (k)

Eleventh attempt
G	C	A	T	C	G	C	A	G	A	G	A	G	T	A	T	A	C	A	G	T	A	C	G
														1
													G	C	A	G	A	G	A	G

Shift by: 1 (k)

Twelfth attempt
G	C	A	T	C	G	C	A	G	A	G	A	G	T	A	T	A	C	A	G	T	A	C	G
															1
														G	C	A	G	A	G	A	G

Shift by: 1 (k)

Thirteenth attempt
G	C	A	T	C	G	C	A	G	A	G	A	G	T	A	T	A	C	A	G	T	A	C	G
																1
															G	C	A	G	A	G	A	G

Shift by: 1 (k)

Fourteenth attempt
G	C	A	T	C	G	C	A	G	A	G	A	G	T	A	T	A	C	A	G	T	A	C	G
																	1	2	3	4
																G	C	A	G	A	G	A	G

Shift by: 2 (l)

The Not So Naive algorithm performs 27 character comparisons on the example.