Abstract: Spaced seeds greatly improve the sensitivity of bio-sequences alignment, but they are not applicable for the sequences containing many insertions and deletions．Based on spaced seeds, we propose seeds with insertions and deletions (Indel seeds), which improves the sequences alignment sensitivity more. Experiments show that adopting optimal search algorithm can find optimal indel seeds under given constraints, further more, indel seeds have higher bio-sequences alignment sensitivity than that of spaced seeds.