Alignment formats may also be used as if they were multiple unaligned sequences by programs doing sequential, database-style access.
There is no provision for enforcing that single unaligned sequence formats are single sequence only. The software will happily try to read more than one sequence if your file contains more than one. However, this may not be what you expected.
Staden experiment file format is parsed as if it were an EMBL file. There is one wrinkle in this. Staden experiment files unfortunately use '-' characters to indicate 'N' -- i.e., that a base is present in a sequence read, but its identity is unknown. Therefore, the software replaces any '-' in an EMBL sequence with an 'N'. Sometimes people use the unaligned formats to distribute aligned sequences by including gap characters. If EMBL files are used i this way for aligned strings, they must use a different character than '-' to indicate gaps.