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. Author manuscript; available in PMC: 2022 Jun 13.
Published in final edited form as: Curr Protoc. 2021 Jun;1(6):e154. doi: 10.1002/cpz1.154

Figure 6.

Figure 6.

Alignment of example2 in HTML format. A) HTML alignment format. The bracket indicates a possible subfamily as observed by the divergence pattern differences for sequences. Each sequence is represented by a single row (sorted by start position) where the color gradient indicates alignment quality (red=low; blue=high) over 10bp non-overlapping windows. The length of the HTML alignment is 242 bp, including the H-pad. B) Terminal output of bestwindow.pl. The highest scoring 10 sequences are shown. C) Terminal output of preprocessAlignments.pl. Note that the consensus range length may differ slightly from your terminal output.