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There are no consistent sequence changes between JJW and AV95, although there are hot spots where amino acid changes occur more frequently in both subjects, especially in the V1 region (see green highlighted amino acids in the alignment below).
We divide the events of the KZR analysis into the following two groups: (1) events belonging to the focal alignment just below KZR, with an azimuth parallel to the focal alignment below this station (N22°W-N8°E) (Group-I); and (2) other events (Group-II) (Fig. 1(b)).
Farther northeast, the freeway heads into an alignment below street level and comes to an interchange with DE 52.
Due to the highly divergent rates of evolution of the ITS region, a set of 16 constant characters was added to replace the 5.8S rDNA region across all taxa, serving as an anchor to make sure that SATé kept the ITS1 and ITS2 separate for the subsequent so-called "anchored ITS" alignment (below).
In this experiment, we used only alignments with sequence identity in the reference alignment below 30%.
(B ) Alignment of yeast and human StART-like domains with Bet-v1 and seven human StARTs, with CLUSTALX coloring of conserved residues, together with secondary structure (above, sheets blue arrows, helices red) and quality of alignment (below).
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(A decent approximation given true-positive rates of >99% in our quality filtered alignments, see Counting False Alignments below).
Alignments below 150 bp in length were discarded.
In both cases, ties are broken arbitrarily and alignments below a certain length are not considered.
Interestingly, non-significant alignments (below the significant threshold) are often found in conventional BLAST searches.
We also removed low percentage identity alignments (below 75%) that overlapped Alu elements.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com