| Polymorphic Malware 1 | Pairwise Alignment | Gap Open Penalty | Gap Extend Penalty | Identity Percentage | Similarity Percentage | Gaps Percentage | Alignment Length | Alignment Score |
| JS. Cassandra Virus | Original JS. Cassandra virus and Variant 1 | 15 | 1 | 98.51% | 98.51% | 1.49% | 134 | 116.00 |
| 20 | 0.5 | 98.51% | 98.51% | 1.49% | 134 | 111.50 | ||
| 20 | 1 | 98.51% | 98.51% | 1.49% | 134 | 111.00 | ||
| 25 | 0.5 | 100.00% | 100.00% | 0.00% | 108 | 108.00 | ||
| 25 | 1 | 100.00% | 100.00% | 0.00% | 108 | 108.00 | ||
| Variant 1 and Variant 2 | 15 | 1 | 88.84% | 88.84% | 11.16% | 215 | 139.00 | |
| 20 | 0.5 | 88.84% | 88.84% | 11.16% | 215 | 140.00 | ||
| 20 | 1 | 100.00% | 100.00% | 0.00% | 138 | 138.00 | ||
| 25 | 0.5 | 100.00% | 100.00% | 0.00% | 138 | 138.00 | ||
| 25 | 1 | 100.00% | 100.00% | 0.00% | 138 | 138.00 | ||
| Variant 2 and Variant 3 | 15 | 1 | 100.00% | 100.00% | 0.00% | 106 | 106.00 | |
| 20 | 1 | 100.00% | 100.00% | 0.00% | 106 | 106.00 | ||
| 25 | 0.5 | 100.00% | 100.00% | 0.00% | 106 | 106.00 | ||
| 25 | 1 | 100.00% | 100.00% | 0.00% | 106 | 106.00 | ||
| Variant 3 and Variant 4 | 10 | 1 | 95.19% | 95.19% | 4.81% | 208 | 170.00 | |
| 15 | 0.5 | 95.19% | 95.19% | 4.81% | 208 | 164.00 | ||
| 15 | 1 | 95.19% | 95.19% | 4.81% | 208 | 160.00 | ||
| 20 | 0.5 | 95.19% | 95.19% | 4.81% | 208 | 154.00 | ||
| 20 | 1 | 95.19% | 95.19% | 4.81% | 208 | 150.00 | ||
| 25 | 0.5 | 95.19% | 95.19% | 4.81% | 208 | 144.00 | ||
| 25 | 1 | 95.19% | 95.19% | 4.81% | 208 | 140.00 | ||
| Variant 4 and Variant 5 | 10 | 1 | 100.00% | 100.00% | 0.00% | 198 | 198.00 | |
| 15 | 1 | 100.00% | 100.00% | 0.00% | 198 | 198.00 | ||
| 20 | 1 | 100.00% | 100.00% | 0.00% | 198 | 198.00 | ||
| 25 | 0.5 | 100.00% | 100.00% | 0.00% | 198 | 198.00 | ||
| 25 | 1 | 100.00% | 100.00% | 0.00% | 198 | 198.00 | ||
| Polymorphic Malware 2 | Pairwise Alignment | Gap Open Penalty | Gap Extend Penalty | Identity Percentage | Similarity Percentage | Gaps Percentage | Alignment Length | Alignment Score |
| W32.CTX/W32.Cholera Virus | Original W32.CTX virus and Variant 1 | 25 | 1 | 99.29% | 99.29% | 0.71% | 1553 | 1507.00 |
| Variant 1 and Variant 2 | 5 | 1 | 96.15% | 96.15% | 3.85% | 2309 | 2015.00 | |
| Variant 2 and Variant 3 | 10 | 1 | 96.41% | 96.41% | 3.59% | 2060 | 1804.00 | |
| Variant 3 and Variant 4 | 5 | 1 | 94.40% | 94.40% | 5.60% | 2017 | 1707.00 | |
| Variant 4 and Variant 5 | 10 | 1 | 100.00% | 100.00% | 0.00% | 736 | 736.00 | |
| 15 | 1 | 100.00% | 100.00% | 0.00% | 736 | 736.00 | ||
| 20 | 0.5 | 100.00% | 100.00% | 0.00% | 736 | 736.00 |