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In this case, CORAL validates the structural alignment and extends the aligned region.
If the alignment score exceeds the user-defined threshold, the aligned region plus the remainder after the alignment are removed.
Each alignment was check manually in MEGA 5 [ 21], alignments with poor quality or aligned region <100 bp were discarded.
This description should make it clear that the alignments are reshuffled over the entire aligned region encompassing all of the domains.
In order to exclude low quality alignments, the orthologous genes with the aligned region <100 bp were discarded for further analyses.
A valid alignment satisfies the following criteria: 1) the similarity between aligned region is ≥ mi n s, 2) the length of the aligned region is ≥ mi n ol, and 3) the overhang of the alignment is ≤ ma x oh.
Similarity of the inverted alignment and coverage of the inverted region to the forwardly aligned region were 100%.
For several MIRNA arm-gene alignments, including those containing miR778, miR780, miR824 and miR856 sequences, the aligned region containing miRNA sequences was clearly more conserved than the remaining arm segments (Figure 5).
As a result, the overlap causes the larger aligned region of energy bands, which is shown in Fig. 7a.
This will select all of the amino acids in the not-so-well aligned region from the beginning up to this point.
All variable sites were included, and so was an ambiguously aligned region of trnH-psbA previously excluded from phylogenetic analysis.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com