The input sequence is piped through the Readseq program prior to being analyized. The Readseq program is developed and produced by Don Gilbert, Biology Department, Indiana University. The program is available from the IUbio archive site.
The allowable input sequence formats are listed below:

IG/Stanford Olsen GenBank/GB Phylip3.2
NBRF Phylip EMBL Plain/Raw
GCG PIR/CODATA DNAStrider MSF
Fitch PAUP/NEXUS Pearson/Fasta Zuker

Note: READSEQ requires a minimum sequence length of 111 bps. for a Plain/Raw sequence to be recognized.
If you are trying to submit plain/raw sequence shorter than this, make it FASTA by simply adding a first line consisting of a ">". 

        For Example:

            Unaccepted                Accepted FASTA
            Short Sequence            Short Sequence

            ACGTGGGTGGGGG             >sample
            GGGGGGAC                  ACGTGGGTGGGGG
                                      GGGGGGAC