So I have used Clustal Omega to do a multiple alignment and hmmbuild to create a hmmer profile for 10000 copies of the same repeat region (30bp long) however when the output is viewed as a hmm logo it is 1200 bases long. I was wondering why this is and if anyone knows a way to get around this?
Used default Clustal Omega options and default hmmbuild options.
Used default Clustal Omega options and default hmmbuild options.