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The number and average of amplicons (alleles) per primer pairs and the polymorphism information content (PIC) value of each loci were estimated using Power-Marker version 3.25 (Liu and Muse 2005).
Loci within the telomeric band are flagged and the proximity of each loci to the centromeres is indicated in Table 4.
The discriminatory nature of each loci were, based on HGDI values, considered as highly >0.6, moderately 0.3 0.6 and poorly <0.3 as suggested by Sola et al. [24].
Discriminatory power of VNTR-based methods depends on the number and set of VNTR loci used; also, there is evidence that the discriminatory power of each loci may vary within each genetic family [50].
The contribution of each loci to the final variance was computed by comparing models with and without the given term.
Expression values were assigned for each family instead of each loci due to high similarity in mature miRNA sequences.
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The performance of each locus was evaluated by calculating the average error (Ea) among the samples (see equation 2).
Ping-containing reads of each locus were extracted from the RelocaTE2 results and the reads were aligned to the Nipponbare Ping element using BWA with default parameters (mem -k 19 -w 100 -T 30).
The primary transcripts are positioned at the top of each locus entry.
To narrow down the candidate region of GL3b and GL6, we performed genetic mapping using recombinant lines of each locus.
The Δ SNP-index) of each locus was calculated by subtraction of the SNP-index of the T-pool from that of the S-pool.
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