A probe system comprising: (a) a population of nucleic acid molecules that have an extendible 5' or 3' end; (b) a first set of barcoded particles that each have a nucleotide sequence comprising in order: (i) a binding sequence that is complementary to the extendible end of the nucleic acid molecules of (a), (ii) a unique particle identifier sequence, and (iii) a first template sequence; wherein each particle can be distinguished from each other particle by their unique identifier sequences; (c) a second set of barcoded particles that each have a nucleotide sequence comprising: (i) the first template sequence, and (ii) a unique particle identifier sequence, wherein the nucleotide sequence of the second set of barcoded particles does not contain the binding sequence and wherein each particle can be distinguished from each other particle by their unique identifier sequences; wherein extension of the nucleic acid molecules of (a) by primer extension if the nucleic acid molecules have an extendible 3' end or gap-fill ligation if the nucleic acid molecules have an extendible 5' end using the first set of barcoded particles of (b) as a template produces first extension products that contain the complement of a unique particle identifier sequence of a particle of (b)(ii) and the complement of the first template sequence of the particles of the first set and of the second set; and wherein extension of the first extension products by primer extension if the nucleic acid molecules have an extendible 3' end or gap-fill ligation if the nucleic acid molecules have an extendible 5' end using the second set of barcoded particles as a template produces second extension products that contain the complement of a unique particle identifier sequence of a particle of (c)(ii), the complement of the first template sequence and the complement of a unique particle identifier sequence of a particle of (b)(ii). (a) a population of nucleic acid molecules that have an extendible 5' or 3' end; (b) a first set of barcoded particles that each have a nucleotide sequence comprising in order: (i) a binding sequence that is complementary to the extendible end of the nucleic acid molecules of (a), (ii) a unique particle identifier sequence, and (iii) a first template sequence; wherein each particle can be distinguished from each other particle by their unique identifier sequences; (i) a binding sequence that is complementary to the extendible end of the nucleic acid molecules of (a), (ii) a unique particle identifier sequence, and (iii) a first template sequence; wherein each particle can be distinguished from each other particle by their unique identifier sequences; (c) a second set of barcoded particles that each have a nucleotide sequence comprising: (i) the first template sequence, and (ii) a unique particle identifier sequence, wherein the nucleotide sequence of the second set of barcoded particles does not contain the binding sequence and wherein each particle can be distinguished from each other particle by their unique identifier sequences; (i) the first template sequence, and (ii) a unique particle identifier sequence, wherein the nucleotide sequence of the second set of barcoded particles does not contain the binding sequence and wherein each particle can be distinguished from each other particle by their unique identifier sequences; wherein extension of the nucleic acid molecules of (a) by primer extension if the nucleic acid molecules have an extendible 3' end or gap-fill ligation if the nucleic acid molecules have an extendible 5' end using the first set of barcoded particles of (b) as a template produces first extension products that contain the complement of a unique particle identifier sequence of a particle of (b)(ii) and the complement of the first template sequence of the particles of the first set and of the second set; and wherein extension of the first extension products by primer extension if the nucleic acid molecules have an extendible 3' end or gap-fill ligation if the nucleic acid molecules have an extendible 5' end using the second set of barcoded particles as a template produces second extension products that contain the complement of a unique particle identifier sequence of a particle of (c)(ii), the complement of the first template sequence and the complement of a unique particle identifier sequence of a particle of (b)(ii).