A method for analyzing single-stranded nucleic acid target sequences in a sample, comprising: (a) contacting a sample comprising a first single-stranded nucleic acid target sequences and at least a second single-stranded nucleic acid target sequence, with detection reagents in a single tube, said detection regents comprising sets of probe-pairs for each of the target sequences, each of said probe-pairs comprising: (i) at least one quencher probe labeled with a non-fluorescent quencher, and (ii) at least one signaling probe labeled with a fluorescent dye, wherein the signaling probe is a self-quenching probe that comprises a non-fluorescent quencher to reduce the signal from the fluorophore when the signaling probe is not hybridized to a target and wherein background signal is emitted from the signaling probe when the signaling probe is not bound to the target sequence, wherein above background signal is emitted from the signaling probe when the signaling probe is bound to the target sequence but the quencher probe is not bound to the target sequence, wherein the signaling probe and the quencher probe hybridize adjacently on the target sequence such that the signal from the signaling probe is quenched by the non-fluorescent quencher when both the signaling probe and the quencher probe are bound to the target sequence; wherein the signaling probes of each of the probe sets are labeled with fluorescent dyes of the same color; wherein the range of temperatures over which the set of probes for said first target bind to the first single-stranded nucleic acid target sequence overlaps with the range of temperatures over which the set of probes for said second target bind to the second single-stranded nucleic acid target sequence. (b) analyzing the signal from the signaling probes as a function of temperature, wherein the signaling probe and quencher probe of a first probe set have melting temperatures for hybridization to a first target sequence in the range of 10-75°C, whereby the first target sequence is a portion of the M. tuberculosis inhA promotor gene and, wherein a first set of the probe-pairs comprises a signaling probe that has a sequence of SEQ ID NO:19 and a quencher probe that has a sequence of SEQ ID NO:20. (a) contacting a sample comprising a first single-stranded nucleic acid target sequences and at least a second single-stranded nucleic acid target sequence, with detection reagents in a single tube, said detection regents comprising sets of probe-pairs for each of the target sequences, each of said probe-pairs comprising: (i) at least one quencher probe labeled with a non-fluorescent quencher, and (ii) at least one signaling probe labeled with a fluorescent dye, wherein the signaling probe is a self-quenching probe that comprises a non-fluorescent quencher to reduce the signal from the fluorophore when the signaling probe is not hybridized to a target and wherein background signal is emitted from the signaling probe when the signaling probe is not bound to the target sequence, wherein above background signal is emitted from the signaling probe when the signaling probe is bound to the target sequence but the quencher probe is not bound to the target sequence, wherein the signaling probe and the quencher probe hybridize adjacently on the target sequence such that the signal from the signaling probe is quenched by the non-fluorescent quencher when both the signaling probe and the quencher probe are bound to the target sequence; wherein the signaling probes of each of the probe sets are labeled with fluorescent dyes of the same color; wherein the range of temperatures over which the set of probes for said first target bind to the first single-stranded nucleic acid target sequence overlaps with the range of temperatures over which the set of probes for said second target bind to the second single-stranded nucleic acid target sequence. (i) at least one quencher probe labeled with a non-fluorescent quencher, and (ii) at least one signaling probe labeled with a fluorescent dye, (b) analyzing the signal from the signaling probes as a function of temperature, wherein the signaling probe and quencher probe of a first probe set have melting temperatures for hybridization to a first target sequence in the range of 10-75°C, whereby the first target sequence is a portion of the M. tuberculosis inhA promotor gene and, wherein a first set of the probe-pairs comprises a signaling probe that has a sequence of SEQ ID NO:19 and a quencher probe that has a sequence of SEQ ID NO:20.