For the align format each line has to begin with a ">" followed by the sequence. All sequences must have the same length, and may consist of upper and/or lower case letters. (The sequences here are from SRP database). The letters for protein sequences as defined in the alphabet file with ``-'' to indicate gaps.

> MVYVDSWEEFVERSVQLFRGDPNATRYVMKYRHCEGKLVLKVTDDRECLKFKTDQAQDAKKMEKLNNIFFALMTRG
> MTYFTSWDEFAKAAERLHSANPEKCRFVTKYNHTKGQLVLKLTDDVVCLQYSTNQLQDVKKLEKLSSTLLRGIVTQ
> -AQYQTWEEFSRAAEKLYLADPMKARVVLKYRHSDGSLCIKVTDDLVCLVYRTDQAQDVKKIEKFHSQLMRLMVAK
> MPQFQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKFHSQLMRLMVAK
> -PQYQTWEEFSRAAEKLYLADPMKARVVLKYRHSDGNLCVKVTDDLVCLVYKTDQAQDVKKIEKFHSQLMRLMVAK