The controller effectiveness is shown through numerical simulations and confirmed using a software simulator and real tests.
Hypocotyl length was first crudely measured using a 0.5 mm marks, and subsequently confirmed using the software Leica Application Suite (Version 2.8.1, Leica Microsystems CMS, GmBH, Switzerland) with seedlings photographed using a Leica stereomicroscope (Leica MZ 12.5) equipped with a Leica DFC420 digital camera.
Relevant ORFs were aligned against ChchNPV and TnSNPV genomes, and PsinSNPV-IE gene models confirmed using Artemis software [ 63].
The ambiguous bases from the 5′ and 3′ terminal sequences were eliminated, and the resulting sequences were confirmed using BioEdit software.
Consensus repeats in the IRs were confirmed using DNAMAN software (for windows, version 2.6) [ 49], and those harboring "G-string" [ 9] were considered as candidate ORB elements.
This pathway analysis finding was confirmed using DAVID software, which was also used to perform additional pathway analyses on the predicted mRNA targets for each of the ten other miRNA families (ESM Table 1).
Analysis was restricted to true biological trios (≥80% probability of being true parent-offspring trios) confirmed using the Nuclear software package [25].
Sequence analysis, confirmed using BPROM online software (Prediction of bacterial promoters, Softberry, http://linux1.softberry.com), indicates the presence of putative -35 (GTGAGT) and -10 (TATAAT) box motifs 151- and 127-bp, respectively, upstream of the putative start codon with a putative ribosomal binding site (AGAGA) 11-bp upstream of the start codon.
Nevertheless, whenever resequenced data were available (i.e., 1000 Genomes Project data), the presence/absence of the duplication was further confirmed using the HMMCopy software (Ha et al. 2012) (fig. 1 and supplementary material and fig. S2, Supplementary Material online).
Bayesian analyses were performed using 2 million generations (one cold and three incrementally heated Markov chains, random starting trees for each chain), and trees were sampled every 100 generations with a final 25% burn-in (convergence was confirmed using Tracer v1.5 software; Drummond and Rambaut 2007).
The authenticity and size of the PCR products were confirmed using a melting curve analysis (using software provided by Applied Biosystems) and a gel analysis.
