Cross Index of Recognition Sequences

Sequences at the top of each column are written 5´ to 3´ according to convention. Open squares at the left of each row are place holders for nucleotides within a restriction endonuclease recognition sequence; arrowheads indicate the point of cleavage. Sequences of complementary strands and their cleavage sites are implied.

blue type = enzymes that recognize only one sequence
black type = enzymes that recognize multiple sequences (degenerate)

Tetra- and Hexa-Nucleotide Recognition Sequences | Penta-Nucleotide Recognition Sequences

Palindromic Tetra- and Hexa-Nucleotide Recognition Sequences

	AATT	ACGT	AGCT	ATAT	CATG	CCGG	CGCG	CTAG	GATC	GCGC	GGCC	GTAC	TATA	TCGA	TGCA	TTAA
	MluCI				FatI				BfuCI DpnII MboI Sau3AI
		HpyCH2IV			CviAII	MspI HpaII		BfaI		HinP1I		Csp6I CviQI		TaqαI		MseI
			AluI  CviKI-1				BstUI		DpnI		HaeIII PhoI  CviKI-1	RsaI			HpyCH4V
									BstKTI	HhaI
		TaiI			NlaIII
	AATT	ACGT	AGCT	ATAT	CATG	CCGG	CGCG	CTAG	GATC	GCGC	GGCC	GTAC	TATA	TCGA	TGCA	TTAA
A  T	ApoI		HindIII*		PciI  AflIII	AgeI*+  BsrFI BsaWI	MluI  AflIII	SpeI*+	BglII  BstYI			TatI
A T		AclI												ClaI BspDI		AseI
A T				SspI*						AfeI	StuI	ScaI*+
A  T
AT					NspI					HaeII					NsiI
	AATT	ACGT	AGCT	ATAT	CATG	CCGG	CGCG	CTAG	GATC	GCGC	GGCC	GTAC	TATA	TCGA	TGCA	TTAA
C G	MfeI*+				NcoI*+  StyI* BtgI BsaJI	TspMI XmaI AcoI  AvaI BsaJI BsoBI	BsaJI BtgI	AvrII BsaJI  StyI*			EagI*  EaeI	BsiWI	SfcI	PaeR7I TliI XhoI+  AvaI BsoBI SmlI	SfcI	AflII  SmlI
C G				NdeI		BmeT110I								BmeT110I
C G		PmlI  BsaAI	PvuII*  MspA1I			SmaI	MspA1I
C G							SacII		PvuI*  BsiEI		BsiEI
CG															PstI*
	AATT	ACGT	AGCT	ATAT	CATG	CCGG	CGCG	CTAG	GATC	GCGC	GGCC	GTAC	TATA	TCGA	TGCA	TTAA
G C	EcoRI*+  ApoI					NgoMIV  BsrFI	BssHII	NheI*+	BamHI*  BstYI	KasI  BanI	PspOMI	Acc65I  BanI		SalI*+	ApaLI
G C		BsaHI								NarI  BsaHI			AccI	AccI
G C		ZraI	Ecl136II Eco53KI	EcoRV*+	Cac8I	NaeI Cac8I	Cac8I	Cac8I	NlaIV	SfoI NlaIV	NlaIV	NlaIV	BstZ17I Hpy8I Hpy166II	HincII Hpy8I Hpy166II	Hpy8I Hpy166II	HpaI HincII Hpy8I Hpy166II
G C
GC		AatII	SacI* BanII BsiHKAI Bsp1286I		SphI*  NspI			BmtI*		BbeI  HaeII	ApaI  BanII BaeGI Bsp1286I	KpnI*+			BaeGI Bsp1286I BsiHKAI
	AATT	ACGT	AGCT	ATAT	CATG	CCGG	CGCG	CTAG	GATC	GCGC	GGCC	GTAC	TATA	TCGA	TGCA	TTAA
T A					BspHI	BspEI  BsaWI AcoI		XbaI+	BclI *		EaeI	BsrGI TatI
T A					Hpy188III	Hpy188III	Hpy188III	Hpy188III						BstBI
T A		SnaBI  BsaAI					NruI			FspI	MscI		PsiI			DraI
T A
TA

* HF (high fidelity) versions of these enzymes are available for simplified reactions and reduced star activity, at no additional cost.

+ A RE-Mix version of this, or the HF version of this enzyme is available.

Palindromic Penta-Nucleotide Recognition Sequences

	AATT	ACGT	AGCT	ATAT	CATG	CCGG	CGCG	CTAG	GATC	GCGC	GGCC	GTAC	TATA	TCGA	TGCA	TTAA
N						BssKI StyD4I						MaeIII
N								DdeI	HinfI		Sau96I
N						ScrFI				Fnu4HI	BmgT120I
N		HpyCH4II												Hpy188I
N											FmuI
N
	AATT	ACGT	AGCT	ATAT	CATG	CCGG	CGCG	CTAG	GATC	GCGC	GGCC	GTAC	TATA	TCGA	TGCA	TTAA
A T						PspGI
A  T									TfiI	ApeKI TseI	AvaII
A T						BstNI
A  T
A  T
A  T							Hpy99I
	AATT	ACGT	AGCT	ATAT	CATG	CCGG	CGCG	CTAG	GATC	GCGC	GGCC	GTAC	TATA	TCGA	TGCA	TTAA
G  C												Tsp45I
G  C
G C						NciI
G  C
G  C										TauI BspUI
G  C