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Can someone explain it clearly. I know that port numbers are used by applications to differentiate which services you have requested, and routing protocols use protocol numbers in TCP header.

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The protocol number is used by the the layer-3 protocol (IPv4 or IPv6) to determine to which layer-4 protocol in the network stack it should send the payload of the packet.

A port number is an address for some layer-4 protocols (TCP or UDP). The port number is used by the layer-4 protocol to determine which application gets the payload of the layer-4 datagram.

And routing protocol use protocol number in TCP header.

I believe you are confusing layer-3 and layer-4. The TCP header (layer 4) doesn't have a field for protocol number - the protocol number is in the IP header (layer 3).

Layers 2 to 4 each encapsulate the datagram of the layer above inside headers for the layer. See this question and answer for more detail

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