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| Parameter | Value |
| Homology matrix | blosum 30 |
| Gap to gap penalty | 0 |
| Gap to aa penalty | −4 |
| Component averaging (k) | 5 |
| Final averaging (gamma) | 20 |
| Sim score weight | 10 |
| Struc score weight | 1 |
| Hydro score weight | 5 |
