I am using RepeatMasker only to find regions of low-complexity regions of DNA. With the default settings "100 bp stretch of DNA is masked when it is >87% AT or >89% GC, a 30 bp stretch has to contain 29 A/T (or GC) nucleotides. ". What can I do to loosen this criteria and play around with the settings?
Perhaps there is better program for what I want to accomplish? I have a list of 60000 rather short sequences (every sequence is about 600 bases).
Thanks
Perhaps there is better program for what I want to accomplish? I have a list of 60000 rather short sequences (every sequence is about 600 bases).
Thanks
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