A method for multiplexed detection of a nucleic acid sequence in a sample comprising: obtaining a plurality of oligonucleotide target-specific probes (TSPs), wherein each of the TSPs is configured to bind to a distinct target nucleic acid sequence, and wherein each of the TSPs comprises: at least one target-binding region configured to bind to at least a portion of the distinct target nucleic acid sequence; at least one common primer-binding region; and one or more copies of a first fluorescent probe binding region and one or more copies of a second FP binding region, wherein a predetermined ratio of the one or more copies of the first FP binding region to the one or more copies of the second FP binding region is indicative of the distinct target nucleic acid sequence the TSP is configured to bind to; contacting the plurality of TSPs with the nucleic acid sequence in the sample such that at least one of the TSPs binds to at least a portion of the nucleic acid sequence and such that a TSP-nucleic acid sequence complex is formed; ligating the at least one of the TSPs bound to at least a portion of the nucleic acid sequence such that a ligated TSP is formed; generating target-specific oligonucleotide sequences (TSSs) by a nucleic acid amplification assay, and wherein the ligated TSP is a template for the nucleic acid amplification assay; contacting the TSSs with a plurality of differently labeled fluorescent probes (FPs) such that a TSS-FP complex comprising the TSS and at least one of the first FP and the second FP is generated; measuring a fluorescence ratio; and identifying the nucleic acid sequence based on the florescence ratio, wherein the FPs comprise linear oligonucleotide probes labeled with fluorophores and molecule beacons (MBs) that are hairpin shaped oligonucleotide probes labeled with fluorophores and quenchers, and wherein MBs fluorescence is quenched in a native state and restored upon hybridization to the TSSs. obtaining a plurality of oligonucleotide target-specific probes (TSPs), wherein each of the TSPs is configured to bind to a distinct target nucleic acid sequence, and wherein each of the TSPs comprises: at least one target-binding region configured to bind to at least a portion of the distinct target nucleic acid sequence; at least one common primer-binding region; and one or more copies of a first fluorescent probe binding region and one or more copies of a second FP binding region, wherein a predetermined ratio of the one or more copies of the first FP binding region to the one or more copies of the second FP binding region is indicative of the distinct target nucleic acid sequence the TSP is configured to bind to; at least one target-binding region configured to bind to at least a portion of the distinct target nucleic acid sequence; at least one common primer-binding region; and one or more copies of a first fluorescent probe binding region and one or more copies of a second FP binding region, wherein a predetermined ratio of the one or more copies of the first FP binding region to the one or more copies of the second FP binding region is indicative of the distinct target nucleic acid sequence the TSP is configured to bind to; contacting the plurality of TSPs with the nucleic acid sequence in the sample such that at least one of the TSPs binds to at least a portion of the nucleic acid sequence and such that a TSP-nucleic acid sequence complex is formed; ligating the at least one of the TSPs bound to at least a portion of the nucleic acid sequence such that a ligated TSP is formed; generating target-specific oligonucleotide sequences (TSSs) by a nucleic acid amplification assay, and wherein the ligated TSP is a template for the nucleic acid amplification assay; contacting the TSSs with a plurality of differently labeled fluorescent probes (FPs) such that a TSS-FP complex comprising the TSS and at least one of the first FP and the second FP is generated; measuring a fluorescence ratio; and identifying the nucleic acid sequence based on the florescence ratio, wherein the FPs comprise linear oligonucleotide probes labeled with fluorophores and molecule beacons (MBs) that are hairpin shaped oligonucleotide probes labeled with fluorophores and quenchers, and wherein MBs fluorescence is quenched in a native state and restored upon hybridization to the TSSs.