Im trying to reproduce some results observed at UCSC genome browser on repeats. I was careful about versions of RepeatMasker and RepBase. I understand that UCSC runs RepeatMasker with -s. However when I retrieve DNA sequence from UCSC window and run RepeatMasker on it, I cant find same events that are showed. I was wondering if the RepeatMasker engine may be an issue. Im using NCBI/RMBLAST [ 2.2.27+ ].
Thanks in advance