Exact(4)
There are 11 high homology matches in Brachypodium to this protein but the amino acid sequence outside the TCP domain was conserved sufficiently between CHE and the Bradi3g60350 protein to suggest that the latter protein was a Brachypodium orthologue (Figure S1).
If the regulator, the target gene, and the binding site are conserved sufficiently, the regulation is considered to be conserved and added to the pipeline's output.
Its strategy is to identify highly conserved, sufficiently long sequences (anchors) throughout a concatenated multi-chromosomal genome and then, for each interval between consecutive anchors that exceeds a certain length, to search recursively for additional, less perfectly conserved anchors.
Taking only those with a repeat-unit length of at least 16 bp, 421 pairs of SSRs contained in 342 pairs of orthologs were selected for primer design, and 54 pairs of sequences with conserved, sufficiently long flanking sites were used to design primers successfully (Additional file 1: Table S2).
Similar(56)
The groEL gene is highly conserved but sufficiently variable to form the basis for genetic target design allowing differentiation of the genera Orientia and Rickettsia, as sequence analysis demonstrated 99.5% identity within the current 23 Thai isolates, and 98.8% identity for all available groEL sequences, including those deposited in GenBank.
Then by examining ortholog families in order of decreasing conservation level, the program screens out families that are not sufficiently conserved.
Suitable loci for the discrimination of species clusters must be present in all strains of the species under study, and should be sufficiently conserved that a fragment of each locus can readily be amplified from each species using a single set of primers, but sufficiently diverse that they are useful in resolving species clusters.
The tannase catalytic domains are sufficiently conserved, such that the catalytic triad superimposes well.
The fact that the regions of sequence for primer hybridization in the described method have remained sufficiently conserved since the AMPV and HMPV diverged, should give the best chance of continued detection of current subgroups and of potential unknown or future emerging MPV strains.
Integrases are usually sufficiently conserved to be recognizable.
This problem can be increased if distantly related genomic resources are selected for the search, given that sufficiently conserved regions for primer design tend to rapidly decline.
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