Exonerate produced no alignment results for certain sequences

[kkunwar]

Hi, is there a way to set exonerate to align each input query sequences in ungapped model (which is also the default model), without considering the sequence similarity or sequence length (also for sequences <20 bp for example) I'm trying to do a pairwise alignment of different clipped sequences with some reference Transposable Element sequences to see how good the clipped bases from short PE reads are aligning with reference TEs. It appears that exonerate has a certain threshold for similarity between sequences in order to report the alignment results, is it the case?

Note: "--percent 0" doesn't change anything on the result.

thanks, Kiran