Indeed, when the sequence conservation levels of target sites identified by the two methods were compared, Made1 related targets were found to be significantly less conserved, on average, than miRanda predicted targets (conservation scores: Made1 targets = 0.082±0.017 miRanda targets = 0.319±0.007; t = 11.27 P = 5.7e-29 Student's ttest).
In contrast, coiled-coil regions are well conserved; on average, they are even slightly more conserved than globular domains (3.46 bit for coiled-coils and 3.41 bit for globular, median values).
c Rodent % conserved = Average number of mouse and rat evolutionary conserved TFBS divided by the total number of TFBS for that particular TF.
b Primate % conserved = Average number of chimpanzee and macaque evolutionary conserved TFBS divided by the total number of TFBS predicted for that particular TF.
Although sequence conservation has been used, our method finds sequences which are conserved on average in a promoter region.
We also observed that the sequence of many introns was highly similar between spruce and pine, and that shorter introns were more conserved on average.
The transmembrane domain (400 amino acids) is very well conserved (84% average identity) among proteins belonging to this clade as well as the NBD 1 domain.
HS sites in the human genome were found to be far more conserved, on average, than sites non HS sites: ~13% of HS sites are conserved compared to ~5% of non HS sites.
Such a scenario is supported by some of our results [ 28], where among pairs of phosphorylation sites close to each others, the one with lower stoichiometry is less conserved on average.
According to the WSoP each nucleotide from the alignment is conserved on average in slightly less than half of the other 10 species (4.43 to 5.09 out of 11 and 3.81 to 4.91 out of 11, for Pomago and TBA, respectively) indicating that the genomes diverged relatively fast.
