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HTML alignments of the 3 consensi produced for example3 by ClusterPartialMatchingSubs.pl. A) cluster0; B) cluster1; C) cluster6.. 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. All sequences are in the 5’ to 3’ orientation. The consensi lengths for cluster0, cluster1 and cluster6 are 2124, 1154, and 192, respectively.
