Example: Modular Design

>FASTA sample input

tatttcttagcttgttttttttttgttctatattgttactttgagctatatttcataaca

gcattcacattctttttccatagtcttttttcccttttatattttaatttactgaagtaa

caaatacttccacttctttcttcttcccaccctcctaaatatatccaacatctcattttt

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Zinc Finger Site Type: Nuclease
Selected Module Sets: Barbas , Sangamo , Toolgen
Left Module Count: 3
Spacer Nucleotide Count: 6
Right Module Count: 3
Ignore Asp Overlap:False

Scores provided for all three finger arrays indicate their likelihood of success based on an extensive survey of modularly assembled proteins (see Instructions). A score of 0.59, for example suggests that the protein has a 59% likelihood of recognizing its target, as measured by a bacterial two-hybrid assay. The probability that two arrays will function as a ZFN can be calculated by multiplying the scores obtained for individual zinc finger arrays.

17 tTTTTTTTTGTTCTATATTGTTACTt 42 Right GNN Score: 0.12
17 aAAAAAAAACAAGATATAACAATGAa 42 Left GNN Score: 0.00

FINGER	HELIX	TRIPLET	REFERENCE NUMBER	MODULE SOURCE
Left F1	QRANLRA	AAA	ZF74	Barbas
Left F2	QRANLRA	AAA	ZF74	Barbas
Left F3	QSGNLTE	CAA	ZF89	Barbas
Left F3	QKSNLTI	CAA	ZF121	ToolGen
Left F3	QSSNLTV	CAA	ZF125	ToolGen
Right F1	THLDLIR	ACT	ZF81	Barbas
Right F2	TSGSLVR	GTT	ZF68	Barbas
Right F2	TSGALTR	GTT	ZF32	SGMO
Right F2	HSSSLVR	GTT	ZF111	ToolGen
Right F3	HKNALQN	ATT	ZF88	Barbas

23 tTTGTTCTATATTGTTACTTTGAGCt 48 Right GNN Score: 0.00
23 aAACAAGATATAACAATGAAACTCGa 48 Left GNN Score: 0.12

FINGER	HELIX	TRIPLET	REFERENCE NUMBER	MODULE SOURCE
Left F1	QSGNLTE	CAA	ZF89	Barbas
Left F1	QKSNLTI	CAA	ZF121	ToolGen
Left F1	QSSNLTV	CAA	ZF125	ToolGen
Left F2	QSSNLVR	GAA	ZF63	Barbas
Left F2	QSGNLAR	GAA	ZF18	SGMO
Left F2	QKGNLLR	GAA	ZF116	ToolGen
Left F2	QSSNLTK	GAA	ZF122	ToolGen
Left F2	QKSNLIR	GAA	ZF123	ToolGen
Left F2	QSSNLTR	GAA	ZF124	ToolGen
Left F3	QKSSLIA	ATA	ZF86	Barbas
Right F1	ERSHLRE	AGC	ZF83	Barbas
Right F2	RADALMV	TTG	ZF35	SGMO
Right F3	THLDLIR	ACT	ZF81	Barbas

51 aTTTCATAACAGCATTCACATTCTTt 76 Right GNN Score: 0.00
51 tAAAGTATTGTCGTAAGTGTAAGAAa 76 Left GNN Score: 0.12

FINGER	HELIX	TRIPLET	REFERENCE NUMBER	MODULE SOURCE
Left F1	QRANLRA	AAA	ZF74	Barbas
Left F2	RRDELNV	ATG	ZF87	Barbas
Left F3	TSGSLVR	GTT	ZF68	Barbas
Left F3	QSSALTR	GTT	ZF50	SGMO
Left F3	HSSSLVR	GTT	ZF111	ToolGen
Right F1	TTGALTE	CTT	ZF103	Barbas
Right F2	HKNALQN	ATT	ZF88	Barbas
Right F3	SKKALTE	CAC	ZF90	Barbas

125 aTACTTCCACTTCTTTCTTCTTCCCa 150 Right GNN Score: 0.00
125 tATGAAGGTGAAGAAAGAAGAAGGGt 150 Left GNN Score: 0.59

FINGER	HELIX	TRIPLET	REFERENCE NUMBER	MODULE SOURCE
Left F1	QSSSLVR	GTA	ZF67	Barbas
Left F1	QSGALTR	GTA	ZF13	SGMO
Left F1	QSSSLIR	GTA	ZF126	ToolGen
Left F1	QSSTLTR	GTA	ZF127	ToolGen
Left F2	QSSNLVR	GAA	ZF63	Barbas
Left F2	QSGNLAR	GAA	ZF18	SGMO
Left F2	QKGNLLR	GAA	ZF116	ToolGen
Left F2	QSSNLTK	GAA	ZF122	ToolGen
Left F2	QKSNLIR	GAA	ZF123	ToolGen
Left F2	QSSNLTR	GAA	ZF124	ToolGen
Left F3	RSDELVR	GTG	ZF66	Barbas
Left F3	RSDALTR	GTG	ZF49	SGMO
Left F3	VSSSLRR	GTG	ZF138	ToolGen
Right F1	SKKHLAE	CCC	ZF94	Barbas
Right F2	TTGALTE	CTT	ZF103	Barbas
Right F3	TTGALTE	CTT	ZF103	Barbas

128 cTTCCACTTCTTTCTTCTTCCCACCc 153 Right GNN Score: 0.00
128 gAAGGTGAAGAAAGAAGAAGGGTGGg 153 Left GNN Score: 0.59

FINGER	HELIX	TRIPLET	REFERENCE NUMBER	MODULE SOURCE
Left F1	QSSNLVR	GAA	ZF63	Barbas
Left F1	QRSNLVR	GAA	ZF1	SGMO
Left F1	QKGNLLR	GAA	ZF116	ToolGen
Left F1	QSSNLTK	GAA	ZF122	ToolGen
Left F1	QKSNLIR	GAA	ZF123	ToolGen
Left F1	QSSNLTR	GAA	ZF124	ToolGen
Left F2	RSDELVR	GTG	ZF66	Barbas
Left F2	RSDALSR	GTG	ZF31	SGMO
Left F2	VSSSLRR	GTG	ZF138	ToolGen
Left F3	QSSNLVR	GAA	ZF63	Barbas
Left F3	QSGNLAR	GAA	ZF36	SGMO
Left F3	QKGNLLR	GAA	ZF116	ToolGen
Left F3	QSSNLTK	GAA	ZF122	ToolGen
Left F3	QKSNLIR	GAA	ZF123	ToolGen
Left F3	QSSNLTR	GAA	ZF124	ToolGen
Right F1	DKKDLTR	ACC	ZF79	Barbas
Right F2	SKKHLAE	CCC	ZF94	Barbas
Right F3	TTGALTE	CTT	ZF103	Barbas

133 aCTTCTTTCTTCTTCCCACCCTCCTa 158 Right GNN Score: 0.00
133 tGAAGAAAGAAGAAGGGTGGGAGGAt 158 Left GNN Score: 0.00

FINGER	HELIX	TRIPLET	REFERENCE NUMBER	MODULE SOURCE
Left F1	RKDNLKN	AAG	ZF76	Barbas
Left F2	RKDNLKN	AAG	ZF76	Barbas
Left F3	QLAHLRA	AGA	ZF82	Barbas
Left F3	QSSHLTT	AGA	ZF119	ToolGen
Right F1	TKNSLTE	CCT	ZF96	Barbas
Right F2	TKNSLTE	CCT	ZF96	Barbas
Right F3	SKKALTE	CAC	ZF90	Barbas

136 tCTTTCTTCTTCCCACCCTCCTAAAt 161 Right GNN Score: 0.00
136 aGAAAGAAGAAGGGTGGGAGGATTTa 161 Left GNN Score: 0.00

FINGER	HELIX	TRIPLET	REFERENCE NUMBER	MODULE SOURCE
Left F1	RKDNLKN	AAG	ZF76	Barbas
Left F2	QLAHLRA	AGA	ZF82	Barbas
Left F2	QSSHLTT	AGA	ZF119	ToolGen
Left F3	QLAHLRA	AGA	ZF82	Barbas
Left F3	QSSHLTT	AGA	ZF119	ToolGen
Right F1	QRANLRA	AAA	ZF74	Barbas
Right F2	TKNSLTE	CCT	ZF96	Barbas
Right F3	TKNSLTE	CCT	ZF96	Barbas

140 tCTTCTTCCCACCCTCCTAAATATAt 165 Right GNN Score: 0.00
140 aGAAGAAGGGTGGGAGGATTTATATa 165 Left GNN Score: 0.12

FINGER	HELIX	TRIPLET	REFERENCE NUMBER	MODULE SOURCE
Left F1	RKDNLKN	AAG	ZF76	Barbas
Left F2	RKDNLKN	AAG	ZF76	Barbas
Left F3	RSDKLVR	GGG	ZF58	Barbas
Left F3	RSDHLSR	GGG	ZF51	SGMO
Left F3	RKDHLTR	GGG	ZF131	ToolGen
Left F3	RSDKLNR	GGG	ZF133	ToolGen
Left F3	RRSHLTR	GGG	ZF134	ToolGen
Right F1	QKSSLIA	ATA	ZF86	Barbas
Right F2	TTGNLTV	AAT	ZF77	Barbas
Right F2	VSSNLNV	AAT	ZF137	ToolGen
Right F3	QNSTLTE	CTA	ZF101	Barbas

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Example: OPEN (Oligomerized Pool Engineering)

>FASTA sample input

ccctttcagtttcgtggcgctctcgtcttctcagcttaatataaaaccaaccacacacca

tctacattgccctttcctttcagtttcgtctctcactgctctccttcaacaataatggcg

gcggctgcggcggctccatctccctctttctccaaaaccctatcgtcctcctcctccaaa

tcctccaccctcctccctagatccaccttccctttcccccaccacccccacaaaaccacc

Zinc Finger Site Type: Nuclease
Selected Module Sets: Joung
Left Module Count: 3
Spacer Nucleotide Count: 6
Right Module Count: 3
Ignore Asp Overlap:True

102 cTCCTTCAACAATAATGGCGGCGGCt 127
102 gAGGAAGTTGTTATTACCGCCGCCGa 127

FINGER	POOL	TRIPLET	REFERENCE NUMBER	MODULE SOURCE
Left F1	Pool1	GGA	41	Joung
Left F1	Pool1	GGA	3	Joung
Left F2	Pool2	GAA	111	Joung
Left F3	Pool3	GTT	31	Joung
Right F1	Pool1	GGC	4	Joung
Right F1	Pool1	GGC	37	Joung
Right F2	Pool2	GGC	108	Joung
Right F3	Pool3	GGC	53	Joung