Otherwise, part of the definition line will be interpreted as a sequence. In sequential format all of one sequence is given, possibly on multiple lines, before the next starts. In interleaved format the first part of the file should contain the first part of each of the sequences, then possibly a line containing nothing but a carriage-return character, then the second part of each sequence, and so on. Only the first parts of the sequences should be preceded by names. The alignment is written in blocks of 60 residues.
Every block starts with sequence names.
Very detailed decription of every field in a GenBank record is available here . One of such programs is ReadSeq and it is available as online version here . Phylogeny Inference Package Manual, version 3.5c. Distributed by the author. Dept. of Genetics, Univ. of Washington, Seattle.