Are you using the NEXUS format? This is how the NEXUS example file looks.

BEGIN CHARACTERS;
[You can either use the matchchar option or else include all characters for 
all sequences.]
DIMENSIONS NCHAR=56;
FORMAT DATATYPE=DNA MISSING=? GAP=- MATCHCHAR=. ;
MATRIX


seq_1 ATATACGGGGTTA---TTAGA----AAAATGTGTGTGTGTTTTTTTTTTCATGTGG

seq_2 ......--..A..---...C.----.G...C.A...C..C...C............

seq_3 ..........A..---...T.----.G.............................

seq_4 ..........A..---G...T----..............................A

seq_5 ..........A..---G...G----..............................C

seq_6 ..........A..---G...C----..............................T

seq_7 ..........A..---G....----..............................A

;

END;