Namea
|
20 nt spacer sequenceb
|
Hairpin
|
GC (%)
|
ΔGc
|
---|
11-1
|
TGCAAATCGGAGTAGAAGCG CGG
|
N
|
50
|
−39.6
|
11-2
|
GCCGACGCCGCCCTTGATGG TGG
|
N
|
75
|
−49.0
|
11-3
|
GCGTGAGGAGGAAGCGGCGG TGG
|
N
|
75
|
−47.3
|
11-4
|
TCCTGTCCGAACCGCCCGCC CGG
|
N
|
75
|
−48.4
|
17-4
|
GACGAGGCACCTAGAGACAC TGG
|
N
|
60
|
−35.8
|
17-5
|
CCACTCATCCAGGACGCTAC TGG
|
N
|
60
|
−37.8
|
17-6
|
CGCGAGGCTGCGGCTGCCAC TGG
|
Y
|
80
|
−49.3
|
17-7
|
GACGCCCCATCCCCAACCAC TGG
|
N
|
70
|
−44.7
|
17-8
|
CGAGAGGTCGCTCTCCAAAC TGG
|
Y
|
60
|
−39.3
|
17-9
|
GGCGATGATGAGGAACCAAC TGG
|
N
|
55
|
−39.2
|
17-10
|
CCTGCTCCTGCGCCTTCCAC TGG
|
N
|
70
|
−44.0
|
Degenerated
|
NVH-N2-BNH-N2-H-N5-HHAC TGG
| | | |
-
aThe locations are referred to Fig. 4 for 11-1 to 11-4 and Fig. 5 for 17-4 to 17-10
-
bDisfavored nucleotides are shown in italics
-
cΔG indicates free energy (kcals/mol). The calculation of free energy and prediction of hairpin in 20 nt spacer were performed by primer premier 5.00
-
dH: A/T/C, V: G/A/C, B: G/T/C, N: any nucleotide; the C-terminus TGG or CGG is the PAM motif