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Table 1 Parameters used in miRprimer for calculation of secondary structure score

From: A tool for design of primers for microRNA-specific quantitative RT-qPCR

Parameter

Values

Score

2 nucleotides at 3′-end

0 or 2 Wsa

0.7

1 Wa

1.0

3 nucleotides at 3′-end

0 or 3 Wsa

0.3

1 or 2 Wsa

1.0

0 or 5 Wsa

0.1

5 nucleotides at 3′-end

1 or 4 Wsa

0.5

2 or 3 Wsa

1.0

3′-self-annealing or primer dimer

5 nucleotides

0.1

4 nucleotides

0.2

Less

1.0

Internal self-annealing or primer dimer

8 nucleotides

0.1

7 nucleotides

0.3

6 nucleotides

0.8

Less

1.0

  1. aW: A or T.