I have been working on aptamers, which are nucleotide sequences. They bind to various targets, in my case a particular cell surface receptor. The people associated with the project performed SELEX and they have selected sequences that have affinity for the target. My advisor believes that the sequences could share a particular binding pocket (consensus sequence).
The sequences are mostly 40 nucleotides long but some of them are shorter or longer in length. I have to aligned the sequences in an attempt to identify sequences containing a consensus site. So far I have used both Clustal Omega and Multalin, but the results from them are pretty inconsistent.
Clustal Omega Alignment:
I also aligned a few sequences using a pairwise alignment method, but I found few similar regions among the sequences.
How do I interpret these results from Clustal Omega and Multalin?