Fig. 4
From: REHUNT: a reliable and open source package for restriction enzyme hunting
Good-suffix shift 2 rule. N is the length of the input sequence and M is the length of the enzyme recognition sequence. Sequence (n) and Enzyme (m) represent the nucleotide at the n-th position in the input sequence and the nucleotide at the m-th position in the enzyme recognition sequence, respectively. Sequence (n s , n e ) and Enzyme (m s , m e ) represent nucleotides from the n s -th position to the n e -th position in the input sequence and nucleotides from the m s -th position to the m e -th position in the enzyme recognition sequence, respectively. a Enzyme (3) mismatches Sequence (3), Enzyme (4, 6) is the suffix string of the enzyme recognition sequence, and prefix string Enzyme (1, 2) matches the suffix substring Enzyme (5, 6). b The Enzyme window is moved and Enzyme (1) is aligned to Sequence (5)