align issue (-T and -k options)

[fallinwind]

Hi Toni! I encountered an obstacle when using paladin to align. This is the case; I got many short peptide sequences about 5-50AA. Only length > 15 peptide seqs are mapping when align with default options, I consider it was resulted from score threshold, so I set -T 5（minimum score to output） to align again, the result shows length > 11 are mapping, at last I set -k 5（minimum seed length) and -T 5, there were length>5 mapping result. Therefore, I am curious that seed length set to 5 should be a correct choice, but how to set the minimum score? For short protein sequences, how to select a reasonable score threshold?