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Gap penalty of bulge in relationship with gap size and starting position
| Starting position of bulge (from 5' end of miRNA) | |||||||
|---|---|---|---|---|---|---|---|
| 1 | 2 | 3 | 4 | 5 | >5 | ||
| gap size | 1 | -1 | -1 | -2 | -2 | -5 | -20 |
| 2 | -1 | -1 | -2 | -2 | -5 | -20 | |
| 3 | -2 | -2 | -3 | -3 | -8 | -25 | |
| 4 | -2 | -2 | -3 | -3 | -8 | -25 | |
| >4 | -5 | -5 | -6 | -6 | -10 | -40 | |
