An appliance receives packets that are part of a flow pair, each packet sharing an application protocol. The appliance determines the application protocol of the packets by performing deep packet inspection (DPI) on the packets. Packet sizes are measured and converted into packet size states. Packet size states, packet sequence numbers, and packet flow directions are used to create an application protocol estimation table (APET). The APET is used during normal operation to estimate the application protocol of a flow pair without performing time consuming DPI. The appliance then determines inter-packet intervals between received packets. The inter-packet intervals are converted into inter-packet interval states. The inter-packet interval states and packet sequence numbers are used to create an inter-packet interval prediction table. The appliance then stores an inter-packet interval prediction table for each application protocol. The inter-packet interval prediction table is used during operation to predict the inter-packet interval between packets.