After this, each of the resulting 157 single-protein data sets were concatenated into a single large alignment containing 72 taxa with 41,372 unambiguously aligned amino acid positions (the total percent of alignment positions in the "157-protein" data set that are gaps are shown in supplementary table S1, Supplementary Material online).
However, a glutamate occurs with same frequency at the respective alignment position in the SP family.
These SVRs correspond to 49% of the alignment positions in the data set.
Examination of alignments of the full-length proteins revealed 10 fully conserved residues (R112, G129, N131, R147, G151, E153, N164, Y166, G211, D213 where the numbers refer to the alignment positions in Fig. S2); all were located within the β-domain.
Numbers correspond to sequence alignment positions in Additional files.
The 347 062 SVRs correspond to 49% of the alignment positions in the database.
Notably, this led to the identification of 41 alignment positions in which residues invariable throughout dicots are absent in monocots, and 84 alignment positions in which residues invariable throughout monocots are absent in dicots.
We found that roughly 8%10%% of the alignment positions in each gene sequence yield non-zero hybridization.
This concerned a total of 219 alignment positions in the plastid data (mostly microsatellites) and 42 nucleotides in the nuclear LFY matrix.
Four of the five alignment positions in which multiple putative functional residues are conserved between Hmd enzymes and paralogs cluster into a single distinct region.
To estimate the average divergence between Neandertal and human DNA sequences, we use alignment positions in which the human and chimpanzee genomes differ.
