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Next: -g, Extension max gap, Up: Parameters Previous: -o, Gap open penalty,

-D, Max distance between LTRs, (positive integer)
-d, Min distance between LTRs, (positive integer)
-L, Max LTR Length, (positive integer)
-l, Min LTR Length, (positive integer)

Distance between LTRs is:

\begin{displaymath}Dist=Pos_{3'LTR\_begin}-Pos_{5'LTR\_end}+1\end{displaymath}

The four parameters makes detected models meet common features of LTR retrotransposons.

2009-04-09