Fig. 1.

Putative sequence alignments as tested in simple mode. The alignment process begins with a partial overlap at the 5′ end of the read (A), increasing to a full-length 5′ overlap (B), followed by full overlaps at all positions (C) and finishes with a partial overlap at the 3′ end of the read (D). Note that the upstream ‘adapter’ sequence is for illustration only and is not part of the read or the aligned region