Not getting proper structure from graphviz

I am using graphviz with dot for my project. Here is a link with my current graph.
The blue edges decides the structure of the grpah and the black edges do not (they have constraint=false).
The problem is that the overall graph doesnot look symmetric as the cluster with node N is separate to right and all the black edges are going together through one area and not spread out across the graph. Does anyone know how to solve this.

Can you post your input graph

Can you post your input graph as well?

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