The following default parameters were applied: maximum expectation value, 3; target accessibility – allowed maximum energy to unpair the target site (UPE), 25; flanking length around the target site for target accessibility analysis, 17 bp upstream and 13 bp downstream; and the range of central mismatch leading to translational inhibition, 9 to 11 nt.
The maximum expectations of 3.0 and the target accessibility-allowed maximum energy to unpair the target site of 50 were applied.
The parameters were as follows - Maximum expectation: 3, Length for complementarity scoring: 20, Allowed maximum energy to unpair the target site (UPE): 25, Flanking length around target site for target accessibility analysis: 17 bp, Range of central mismatch leading to translation inhibition: 9 11 nt.
Identified sRNAs with more than 100 reads in the database were further confirmed in the psRNAtarget web server (http://plantgrn.noble.org/psRNATarget) using following parameters: maximum expectation = 5.0, and target accessibility - allowed maximum energy to unpair the target site (UPE) = 50.
E (Expectation): scores < 3.0 considered as a potential target of miRNA; UPE :Target accessibility - allowed maximum energy to unpair the target site.
(UPE ; Maximum energy to unpair the target site, UPE range: 0.0-25.0; E-value range: 0.0-4.0) ThESTST libraries from which the Boechera miRNAs were mined were flower-specific [ 39, 40], and expectedly, a number of identified TF-targeting miRNAs have been associated with flower development in other species.
The maximum energy of unpairing (UPE) the target site was set as 25 kcal [ 64].
To obtain more accurate picture of the birth-and-death evolution of target sites, we reconstructed the ancestral sequence of each target site by using the maximum likelihood method (Yang et al. 1995) and estimated the numbers of potential target sites in ancestral species and gains and losses of the target sites.
MF at the target site is alternative pulses with a maximum flux density of 0.4 T.
We generated a purposive sample of patients and caregivers over a period of 10 weeks to a maximum target of 20 patients and 10 caregivers at each site.
