[Genome] Scone and Insertions and Deletions in ENCODE

[Janis Dingel]

Hi,

does the SCONE score for ENCODE, hg17 regions take insertions and 
deletions into account?
It says under "Description" on the TBA Cons Track Settings site  that  
it does : 
http://gbrowser.bii.a-star.edu.sg/cgi-bin/hgTrackUi?hgsid=20&c=chrX&g=encodeTbaCons
However, I am comparing scores from the TBA Cons Track to the respective 
TBA ENCODE alignments and gaps in the alignment do not seem to have 
influence on SCONE.

Thanks and Best Regards

Janis