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SQL Server Azure virtual machines do not support Failover Cluster Instances

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As of 29/10/2015 BizTalk Server 2013 is not supported with Failover Cluster instances in Windows Azure as it is reflected here:

https://support.microsoft.com/en-us/kb/2721672

If your solution requires high availability using SQL Server FCI, the BizTalk Server 2013 Azure virtual machines should not be used. If your solution does not require high availability by using SQL Server FCI, the BizTalk Server Azure virtual machines may satisfy your solution needs.

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