I am looking for information on JTAG interface on PCI-e 1x connector. Do anyone has an informaton how to program it? I would like to use it to program microcontrollers and FPGAs.
JTAG interface in PCIe connector is optional as per PCI-SIG. They won't define any specifications for these pins. They are defined as per 1149.1.
You have not specified this question in the perspective of addin card or host.
If you want to program devices on JTAG inside Add-in card from Host, then connect this pins to PCIe connector and see support in host side for programming this.
Below is the snap from CEM
While the PCIe connector does have a few pins designated for JTAG, they are virtually never used. In particular, they are never connected to anything on PC motherboards.
If you want to program devices over JTAG, you will need to purchase a JTAG adapter -- these are typically USB devices. The JTAG functionality defined on the PCIe connector will not be of any help to you.
The PCIe JTAG doesn’t have a specific usage definition, nor is it required in the interface. In theory it could be used for board test and programming.
As a practical matter it’s much easier to provide specific JTAG connectors as needed for your application, e.g., microcontroller debug, FPGA programming and such. This kind of approach also avoids signal integrity issues that often bedevil large JTAG daisy-chain routing setups.