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In dehydration-inducible promoters of Arabidopsis, the most conserved sequence (ACACGT), second most conserved sequence (ACGTGT), and other highly conserved sequences were part of ABRE and G box (CACGTG) (Fig. 5B; Supplementary Table S32).
In order to study the benefit of alignment-based conservation analysis, we used phastCons [27] to identify the most conserved sequence fraction that would optimize recall (see Table 2), where this fraction is defined as the percent of nucleic acids in the sequences retained after masking poorly conserved regions.
The 24-amino acid (residues 14 37 underlined in figure 1) region essential for λ CIII activity [13] is the most conserved sequence.
The most conserved sequence stretches were chosen as 5' and 3' targeting sites, and were amplified by PCR from ITG2F6 genomic DNA using the primers shown in Table 1.
To test whether this region contained any element that has enhancer activity, the most conserved sequence within this region, mm8_chr16: 91,029,835 — 91, 029,835 (designated ULTRA), was chosen to test for its activity in ES cells.
The second most conserved sequence (AATATC) was part of EE (Fig. 5A; Supplementary Table S31).
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As a set of sequences with high conservation in eutherian mammals, we used the UCSC phastCons28wayPlacMammal most conserved sequences (PCSs).
Generally, an efficient RT-PCR relies on finding the most conserved sequences across all virus genotypes to use as primers in order to efficiently amplify the maximum number of these diverse genetic variants.
PTP motif 9 (VHCSXGXGR[T/S]G) is one of the most conserved sequences and corresponds to the active site of the enzyme.
cDNA from prostate cancer patients with different genotypes for R462Q, were used to screen an oligonucleotide array containing the most conserved sequences from all known viruses.
Many of the hydrophobic residues map to predicted TMS regions, which are characteristic of all sampled VirB3 proteins, and two motifs within the N-terminal region, "(GAT L ST RP" and "GV", comprise the most conserved sequences of these proteins.
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