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Good multiple alignments tools are required for the generation of better motif descriptors (pat, prf, hmm). However these tools are computer intensive, try to limit yourself...

Tips: ClustalW is faster than T-Coffee, but T-Coffee is more accurate, especially when sequences share less than 30% identity. MAFFT is much faster than ClustalW and T-Coffee and very accurate.

General advices
Input You must paste at least 3 sequences (or identifiers). The limitations, on the upper number of sequences (or identifiers) and the total number of residues allowed, may vary according to the current hardware availability.
Sequence format The input sequences must be in FASTA (Pearson) format.

Example: (cut&paste in the tool text area)

Sequence names Each sequence must have a different name (8 first characters are significants).
Other Avoid special characters, e.g. +"*%&/()!?'@€<>,;:$=|
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Thompson JD, Higgins DG, Gibson TJ.
Nucleic Acids Res. 1994 Nov; 22(22):4673-80.

T-Coffee: A novel method for multiple sequence alignments
C. Notredame, D. Higgins, J. Heringa
Journal of Molecular Biology 2000 Sept; 302(1):205-217.

Improvement in the accuracy of multiple sequence alignment program MAFFT.
K. Katoh, K. Kuma, T. Miyata and H. Toh
Genome Informatics. 2005; 16(1):22-33.
MAFFT version 5: improvement in accuracy of multiple sequence alignment.
K. Katoh, K. Kuma, H. Toh and T. Miyata
Nucleic Acids Res. 2005; 33:511-518.
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
K. Katoh, K. Misawa, K. Kuma and T. Miyata
Nucleic Acids Res. 2002; 30:3059-3066.