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In the Oligo Entry Tool, you will see tabs for 5′ Mods, Internal Mods, and 3′ Mods. Most modifications are not available at the 25 nmol scale, so if you do not see the modification you are looking for you should increase your synthesis scale to at least the 100 nmol scale. This will increase the menu of modification options available.
When you find the modification you need, click its modification code and the tool will add it to your sequence. If the modification is internal you will want to make sure that the entire modification code is inserted into the exact position desired within the sequence.
For more detailed information, see the DECODED article, Ordering modified oligonucleotides.