[EMBOSS] problems with allversusall tool

[laura]

Dear emboss users, 

I am using allversus all tool for global sequence alignment. I am writing
to you because I am obtaining perfect aligments between sequences that have
a very different length.. for example if I have a 100 residues protein
sequence and a 2 residues protein sequence I obtain a 100% identity when I
perform the alignment, in which I would expect a very poor sequence
identity. Is there any way to prevent it or it is a posible bug in the
program?? 

I would thank you to answer me as soon as possible, 

Regards, 

Laura.