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A small fraction, 7/162 (4%) have two sequence regions with significant conservation.
In the 5' upstream regions, we found 33 motifs with significant conservation among the three rodent malaria species.
As above for the total TAIR set, Type 2 is also the most common topology among those with significant conservation in Brassicaceae (Table 1), although Types 1 and 4 also arise for >25% of cases.
Bread wheat (Triticum aestivum L). is an allohexaploid (2n = 6x = 42) containing three related genomes: A, B and D, with significant conservation of gene order between the chromosomes of the respective genomes.
For the TAIR set of cis-NATs, we found that 55/162 (34%) of the cis-NATs had NOLPs with significant conservation (P < 0.05) (or 32/162 [20%] if we apply a Holm-Bonferroni [HB] correction) (Table 1 and Additional file 2).
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Analysis of enrichment of specific DENV genes with clusters of positions with a significant conservation of folding energy signals and distribution of these clusters over different genes can be found in Additional file 1.
Remarkably, most functional classes of proteins with a significant conservation signal were highly specific for the signal within one group of domains, but not in other groups.
Specifically, 53-66 clusters for strong folding and 49-73 clusters for weak folding (depending on serotype) aggregated of positions with a significant conservation of folding energy signals (related to partially overlapping local genomic regions) were recognized.
We suggested that positions along the coding region with a significant conservation of folding associated signals are grouped in 49 - 73 clusters related to partially overlapping local genomic regions that may tend to undergo an evolutionary selection for a strong or weak folding.
The borders of POS6 correlate with the region of significant conservation with promoter regions of INO orthologs in Brassica species.
PCPMer motifs are short contiguous sequences with a statistical significant conservation of physicochemical properties of amino acid residues derived from a multiple sequence alignment of proteins.
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