Split and shifted gaps

In many MSAs both situations will arise: gaps are shifted and split.
Example 2.2:  In the MSA of Figure , sequence A has two gaps and sequence B has three gaps. If we push the gaps together and move them to the same position, we combine 5 events to one single event. In addition, the resulting alignment has a better score (the optimal score in this case) and also makes more sense from a biological point of view.

  

Figure: Here 5 events can be reduced to one event by shifting and fusing the gaps.

Score: 104.635 Score: 240.139 Maximum: 240.139 Maximum: 240.139 Event 1 A: RPC__VCP_VLRQ A: RPCVCP___VLRQ B: RPC_A_CPV_LRQ B: RPCACP___VLRQ C: KPCVCPRQLVLRQ => C: KPCVCPRQLVLRQ D: KPCVCPRQLVLRQ D: KPCVCPRQLVLRQ E: KPCLCPKQAAVKQ E: KPCLCPKQAAVKQ