Fig. 3
From: misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads
Misjoin in scaffold. After aligning the misjoined scaffold to reference, it will be split into two sub-segments according to the alignment information, and the two sub-segments are aligned with different reference strands or aligned to distinct regions with long distance. And these two sub-segments overlap each other due to the repeat (middle thick red lines) whose erroneous tails around margins M L and M R will be trimmed