Table 1.

Tests of reproducibility

Test	Locia	TEb	Number of samples	Difference between replicatesc
				Maximum	Minimum	Mean
Across platesd	SCHRBa_011_K15	scIvana 1.1	22	0.67	0.05	0.29
	SCHRBa_015_O15	scIvana 1.4	21	0.66	0.00	0.21
	SCHRBa_044_D02	scIvana 1.2	17	0.78	0.02	0.28
Across Real-Time PCR systemse	SCHRBa_011_K15	scIvana 1.1	4	0.50	0.07	0.28
	SCHRBa_015_O15	scIvana 1.4	4	0.85	0.34	0.55
	SCHRBa_044_D02	scIvana 1.2	4	1.31	0.44	0.82
Template concentrationf	SCHRBa_044_D02	scIvana 1.2	8	0.81	0.10	0.37
Primer concentrationg	SCHRBa_015_O15	scIvana 1.4	48	0.97	0.02	0.38
	SCHRBa_044_D02	scIvana 1.2	42	0.99	0.01	0.46
Threshold settingh	SCHRBa_011_K15	scIvana 1.1	8	0.17	0.05	0.11
	SCHRBa_015_O15	scIvana 1.4	9	0.27	0.02	0.09
	SCHRBa_044_D02	scIvana 1.2	8	0.23	0.06	0.13

^a The BAC number in which in the scIvana element was identified (de Setta et al., 2014).

^b Name of the TE. scIvana 1.1 and 1.2 have been described previously (Domingues et al., 2012).

^c All results are estimates of the ratio of alleles with the element to alleles without the element and were transformed into a total of 10. Only the figure for the presence of the allele is shown.

^d Master mixes were set up separately and run on two separate plates.

^e Reactions were run on either the Applied Biosystems 7300 or Applied Biosystems ViiA 7 Real-Time PCR systems.

^f Genomic DNA was added at a final concentration of 0.13 or 1.3ng μl^–1.

^g Primers were added at a final concentration of 500nm and optimized. For optimized primer concentrations, see Supplementary Table S2.

^h Threshold settings were set at 0.5, 1.0, and 1.5.