Arrays with quality control tracers

A method of determining the density, the distribution, or the density and the distribution of an untagged primer nucleotide sequence grafted to a support comprising:

• providing the support comprising:
• a plurality of discrete wells;
• a gel material positioned in each of the plurality of discrete wells;
• a quality control tracer grafted to the gel material in each of the plurality of discrete wells;
• and
• the untagged primer nucleotide sequence grafted to the gel material in each of the plurality of discrete wells;
• wherein the quality control tracer comprises:
• a cleavable nucleotide sequence comprising a remaining portion and a cleavable portion, the remaining portion being a non-reactive nucleotide sequence having a first end grafted to the gel material and a second end linked to the cleavable portion, and the cleavable portion including a cleavage site;
• and
• a detectable label attached to a 3′ end of the cleavable nucleotide sequence;
• the cleavable nucleotide sequence being selected from the group consisting of
• 5′-CATCTAGGCATCTAAGCATCAAUCTTACA-3′ (SEQ. ID NO. 3),
• 5′-polyT-CATCTAGGCATCTAAGCATCAAUCTTACA-3′ (SEQ. ID NO. 6),
• 5′-alkyne-CATCTAGGCATCTAAGCATCAAUCTTACA-3′ (SEQ. ID NO. 9),
• 5′-(alkyne)-(polyT or TTTTTT)AATGATACGGCGACCACCGAGAUCACAC-3′ (SEQ. ID NO. 19);
• and
• wherein the quality control tracer and the untagged primer nucleotide sequence are grafted to the gel material in a predetermined ratio;
• detecting a signal from the detectable label;
• determining the density and/or distribution of the quality control tracer based at least in part on the signal from the detectable label;
• and
• determining the density and/or distribution of the grafted untagged primer nucleotide sequence based on the signal from the detectable label and the predetermined ratio.