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Thirdly, RNA structure of the HAmo SINE is obviously composed of three parts: tRNA-related region, a family-specific region and LINE2-related region, that correspond to there parts of secondary structure of its RNA: the cloverleaf structure (the 5'domain), an unstructured region, the extended stem-loop (the 3'domain).
Interestingly, there is also a translocation of the top arm of P4, including markers from the nonrecombining region that correspond to the top of SlChr03/StChr03.
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Previous analyses of R. variegatus revealed two distinct lineages in our study region that corresponded to separate "northern Oregon" and "central Oregon" clades [29].
For peptidases TmL9 and TmB28, there were significant changes in the model structure (less than 90% of amino acids were in a favored region, or some of the amino acids forming the subsites were in outlier region) that corresponded to the major differences in the sequence of the peptidases.
Across all samples, we identified ~100,000 non-redundant FAIRE regions that correspond well to those observed in other breast cell lines and align with known TF binding sites [ 19] (Additional file 1: Figures S1 and S2).
Low complexity regions that corresponded to the mucin domains were predicted by the computer program NetOGlyc 3.1 [ 28].
The cross-sectional IVUS image of the vessel showed two hypo-echoic regions that corresponded to the location of plaques (yellow arrows in Fig. 2(a) ).
This tool also located three low complexity regions that corresponded to the mucin domains predicted by the computer program NetOGlyc 3.1 [ 28].
Next, we analyzed how well protein regions that corresponded to the location of AS events were sampled in each of the experimental sets.
When possible, axolotl and tiger salamander orthologs for each gene in Additional File 5 were aligned via BLAST to identify gene regions that corresponded to the same nucleotides covered by Affymetrix probe-sets.
Most of the non-redundant elements with two identifiable LTRs belonged to the Copia superfamily, but a large proportion of retroelements had non-identifiable internal regions, or regions that corresponded to host genes or other non-LTR TEs as has also been shown for poplar (Additional file 5) [ 57].
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