A chemical reaction never processes completely. Impurities which occur during oligonucleotide synthesis have to be removed.
Using phosphoramidite chemistry, the main side reaction is the formation of n-x products. The longer the sequence, the more n-x products occur. After deprotection, the protecting groups will be part of the raw synthesis product.
Yield [%] CE 99.5%
Yield [%] CE 99.0%
Yield [%] CE 98.5%
20mer
91
83
75
30mer
86
75
65
40mer
82
68
55
60mer
74
55
41
100mer
61
37
22
Theoretical percentage of full length product = coupling efficiency (CE) x (length of oligonucleotide-1)