Method of detecting target nucleic acid molecules

A system for detecting a nucleic acid barcode sequence, the system comprising:

• (a) a padlock probe comprising target binding sites capable of hybridizing to a target sequence in a target nucleic acid molecule,
• wherein the padlock probe comprises a nucleotide barcode sequence that identifies the padlock probe, and wherein the nucleotide barcode sequence comprises a first domain sequence and a second domain sequence, wherein a portion of the first domain sequence overlaps with some but not all of the second domain sequence;
• (b) a universal pool of reporter probes, wherein the universal pool of reporter probes comprises at least two different species of reporter probes, wherein the first species of reporter probe comprises a first optically detectable moiety, and the second species of reporter probe comprises a second optically detectable moiety;
• (c) a first detection probe, wherein the first detection probe comprises (i) a recognition sequence comprising the first domain sequence, and (ii) a first overhang sequence comprising a reporter probe binding site complementary to a reporter probe of the universal pool of reporter probes;
• (c) a second detection probe, wherein the second detection probe comprises (i) a recognition sequence complementary the second domain sequence, and (ii) a second overhang sequence comprising a reporter probe binding site complementary to a reporter probe of the universal pool of reporter probes;
• wherein the second detection probe is capable of initiating a strand displacement reaction to displace the first detection probe hybridized to the first domain.