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Based on our results and those studies, we designed a target sequence with six tandem repeats with perfect complementarity to the mature strand of the miR122 duplex.
The 10 nt motif returned by MEME included a 7 nt stretch with perfect complementarity to positions 2 8 in miR-124.
The next three most highly overrepresented 6mers were overlapping sequences with perfect complementarity to positions 1 8 in miR-1 (Figure 4Ai).
Unexpectedly, we were unable to identify by BLAST a single target transcript with perfect complementarity to any of our recovered shRNA sequences.
To compare preferences to the two ends, we made perfect WC complementarity the second-stage filtering criterion, and sorted the results into one set of potential targets with perfect complementarity to the 5' ends of miRNAs, and another set with perfect complementarity to the 3' ends.
The ratio of the calculated free energy of miRNA: target to the free energy if the miRNA had perfect complementarity to the target gene (percent minimum free energy) was the final feature.
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Potential off-target effects of hpRNAi in plants arise because the large number of sRNAs spawned by the silencing construct may target any gene that shares perfect or near-perfect complementarity to these sRNAs.
The majority of plant miRNAs possess perfect or near-perfect complementarity to their targets [ 45].
A total of 31 miRNA families were found to have perfect or near-perfect complementarity to SmAGOs.
In plants, most miRNAs have perfect or near-perfect complementarity to their mRNA targets and downregulate them by targeted cleavage or translational repression [ 4, 5].
Plant miRNAs recognize their targets through near-perfect complementarity to direct RISC-mediated cleavage, although in some cases translational inhibition and DNA methylation can be the mode of action of miRNA-mediated gene silencing [ 19- 21].
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