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Using the Tandem Repeat Finder Software, a total of 19 microsatellite motifs (di-, tri-, and tetra- repetition) were found in silico in seven of the nine scaffolds published so far.
After data processing by Biomarker Wizard software, a total of 130 peaks were selected.
Using the Protein chip Data Manager software a total of 586 protein peaks were identified and subjected to further statistical analysis.
Using the Trinity transcriptome-assembly software, a total of 120,426 assembled transcripts were obtained from seven sample libraries (untreated control, defoliation, and simulated grazing).
Using MISA software, a total of 13,861 SSRs were available as potential marker loci, being 13,172 SSRs single and 689 compound SSRs for all studied species.
Using the software, a total of 3952 primer pairs were designed for these SSR sequences (information listed in Additional file 1).
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The software predicted a total of 125 SFPs (on average ∼2 per gene), and we could experimentally validate 32 of them (Table 1).
The gene expression analysis with the Chipster software generated a total of 1592 differently expressed genes in the CA1 subregion of KA-treated rats compared to control rats.
The GS Amplicon Variant Analyzer software identified a total of 1714 variants following alignment of the raw sequence data.
The Prodigal software predicted a total of 945,211 genes across all genomes.
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