From Array Suite Wiki
This is the minimal size that a fusion read can be cut to, in order for it to be counted. It is parameter Alpha as described in the FusionMap paper.
For best performance, it should set to Min(25, Max(17,floor(ReadLength/3))).
Set this parameter to 25 to use fixed cut size 25; set it to 0 to use the recommended formula.
Also read: Seed Read