If your traffic traverses autoVPN then my question would be.. do you have 2 ISP's per branch or only 1? If you have 2 you can monitor latency, jitter and load on both lines and even have performance based uplink selection. The way you monitor this is by going to VPN status and on the bottom side of the page you get the uplink decisions list. If you have multiple links you can just click on WAN1 or WAN2 on any of the packets going towards the hub you want to check against. And then you will get that page where you can see the stats between your local MX and remote MX on both uplinks. Alternatively if you want to analyse per packet and CONSTANTLY. Then you'll need to have two capture devices and do ring buffered captures on both ends of the VPN. This means you'll have to mirror the switchport going to the MX'es on both ends. This is laborious but will yield honest and precise results.
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