Hi there,

I am using calcDivergenceFromAlign to calculate k-distance by calcDivergenceFromAlign.pl (script from repeatMasker). However, the result makes me confused.

For example, the smallest LINE/L2 Kimura% is 2.58,

" LINE/L2 rnd-6_family-29449 34415 34101 2.58 "

but the "Coverage for each repeat class and divergence (Kimura)" shows that LINE/L2 have both div 0 and 1.

My question is , is Kimura% not equal to the div catalog? I though that div 0 and 1 should be zero, and begin have value start from div 2.

Thank you for helping.

Best regard, Jui-Hung