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| # Alignment | Alignment location | Similarity | Score* | E-value | Strand | |
| Query (CHV-1) | Subject | ||||||
| HSV-1 | 1 | 100096-100107 RS1 | 123071-123060 RL2 | 12/12 (100%) | 22.9 bits (24) | 6.0 | +/− |
| BoHV-1 | 1 | 99058-99068 RS1 | 101712-101722 RL2 | 11/11 (100%) | 21.1 bits (22) | 3.5 | +/+ |
| SuHV-1 | 1 | 101525-101537 RS1 | 100613-100601 Gen between RL2 and RS1 | 13/13 (100%) | 24.7 bits (26) | 2.6 | +/− |
| 2 | 99116-99127 RS1 | 97541-97530 Gen between RL2 y RS1 | 12/12 (100%) | 22.9 bits (24) | 9.1 | +/− | |
| 3 | 97378-97389 Entre genes RL2 y RS1 | 97785-97796 Gen between RL2 and RS1 | 12/12 (100%) | 22.9 bits (24) | 9.1 | +/+ | |
| 4 | 97412-97423 Entre genes RL2 y RS1 | 97785-97796 Gen between RL2 and RS1 | 12/12 (100%) | 22.9 bits (24) | 9.1 | +/+ | |
| 5 | 97446-97457 Entre genes RL2 y RS1 | 97785-97796 Gen between RL2 and RS1 | 12/12 (100%) | 22.9 bits (24) | 9.1 | +/+ | |
| 6 | 97480-97491 Entre genes RL2 y RS1 | 97785-97796 Gen between RL2 and RS1 | 12/12 (100%) | 22.9 bits (24) | 9.1 | +/+ | |
| 7 | 101539-101553 RS1 | 101946-101932 Gen between RL2 and RS1 | 14/15 (93%) | 22.9 bits (24) | 9.1 | +/− | |
| 8 | 99693-99704 RS1 | 104163-104174 RS1 | 12/12 (100%) | 22.9 bits (24) | 9.1 | +/+ | |
| 9 | 101057-101068 RS1 | 106025-106036 RS1 | 12/12 (100%) | 22.9 bits (24) | 9.1 | +/+ | |
| FeHV-1 | 1 | 97974-99088 RS1 | 107622-108739 RS1 | 713/1125 (63%) | 156 bits (172) | 4e−40 | +/+ |
| 2 | 100014-100486 RS1 | 109800-110275 RS1 | 318/476 (67%) | 145 bits (160) | 6e−37 | +/+ | |
| 3 | 96852-97046 RL2 | 105478-105672 RL2 | 127/195 (65%) | 46.4 bits (50) | 5e−07 | +/+ | |
| 4 | 99691-99703 RS1 | 107176-107188 RS1 | 13/13 (100%) | 24.7 bits (26) | 1.5 | +/+ | |
| 5 | 99682-99704 RS1 | 110364-110386 RS1 | 19/23 (83%) | 24.7 bits (26) | 1.5 | +/+ | |
| 6 | 99923-99934 RS1 | 104517-104506 RL2 | 12/12 (100%) | 22.9 bits (24) | 5.3 | +/− | |
| 7 | 101187-101198 RS1 | 104818-104807 RL2 | 12/12 (100%) | 22.9 bits (24) | 5.3 | +/− | |
| 8 | 100748-100759 RS1 | 109694-109683 RS1 | 12/12 (100%) | 22.9 bits (24) | 5.3 | +/− | |
| 9 | 99316-99330 RS1 | 111198-111184 RS1 | 14/15 (93%) | 22.9 bits (24) | 5.3 | +/− | |
| EHV-1 | 1 | 99990-100507 RS1 | 116550-117067 RS1 | 346/519 (67%) | 149 bits (164) | 6e−38 | +/+ |
| 2 | 96052-96082 RL2 | 111001-111031 RL2 | 24/31 (77%) | 24.7 bits (26) | 1.6 | +/+ | |
| 3 | 96905-96922 RL2 | 111812-111829 RL2 | 16/18 (89%) | 24.7 bits (26) | 1.6 | +/+ | |
| 4 | 98405-98416 RS1 | 112659-112648 Gen between RL2 and RS1 | 12/12 (100%) | 22.9 bits (24) | 5.7 | +/− | |