File S1 - Detection of DNA Sequences Refractory to PCR Amplification Using a Biophysical SERRS Assay (Surface Enhanced Resonant Raman Spectroscopy)

Tables S1–S11. Table S1. Alignment of the sequences obtained from cloning-sequencing for the PCR amplification of the N5′/N3′ molecule. The N molecule is taken as a reference. PCR amplification primers are removed from the analysis and appear only on the template molecule in red. Differences from the initial molecule are represented in red. For each haplotype sequence, the observed frequency and percentage are given. Table S2. Alignment of the sequences obtained from cloning-sequencing for the PCR amplification of the N5′/I3′ molecule. The N5′ and C_I3′ molecules are taken as a reference. The C_I3′ corresponds to I3′ strand in the reverse complementary orientation. Table S3. Alignment of the sequences obtained from cloning-sequencing for the PCR amplification of the II5′/N3′ molecule. The II5′ and C_N3′ molecules are taken as a reference. The C_N3′ corresponds to N3′ strand in the reverse complementary orientation. Table S4. Alignment of the sequences obtained from cloning-sequencing for the PCR amplification of the N5′/IV3′ molecule. The N5′ and C_IV3′ molecules are taken as a reference. The C_IV3′ corresponds to IV3′ strand in the reverse complementary orientation. Table S5. Alignment of the sequences obtained from cloning-sequencing for the PCR amplification of the V5′/N3′ molecule. The V5′ and C_N3′ molecules are taken as a reference. The C_N3′ corresponds to N3′ strand in the reverse complementary orientation. Table S6. Alignment of the sequences obtained from cloning-sequencing for the PCR amplification of the I5′/I3′ molecule. The I5′ and C_I3′ molecules are taken as a reference. The C_I3′ corresponds to I3′ strand in the reverse complementary orientation. Table S7. Alignment of the sequences obtained from cloning-sequencing for the PCR amplification of the II5′/I3′ molecule. The II5′ and C_I3′ molecules are taken as a reference. The C_I3′ corresponds to I3′ strand in the reverse complementary orientation. Table S8. Alignment of the sequences obtained from cloning-sequencing for the PCR amplification of the I5′/IV3′ molecule. The I5′ and C_IV3′ molecules are taken as a reference. The C_IV3′ corresponds to IV3′ strand in the reverse complementary orientation. Table S9. Alignment of the sequences obtained from cloning-sequencing for the PCR amplification of the V5′/I3′ molecule. The V5′ and C_I3′ molecules are taken as a reference. The C_I3′ corresponds to I3′ strand in the reverse complementary orientation. Table S10. Alignment of the sequences obtained from cloning-sequencing for the PCR amplification of the II59/IV39 molecule. The II59 and C_IV39 molecules are taken as a reference. The C_IV39 corresponds to IV39 strand in the reverse complementary orientation. Table S11. Alignment of the sequences obtained from cloning-sequencing for the PCR amplification of the V59/IV39 molecule. The V59 and C_IV39 molecules are taken as a reference. The C_IV39 corresponds to IV39 strand in the reverse complementary orientation. (DOCX)