When you align a sample file to a reference sequence that contains discontinuous segments, such as transcripts or assembled contigs, the breakpoints between segments are indicated by a vertical red line in the Whole Genome viewer and in the Alignment viewer. Because the sequence from the end of one to segment to the beginning of the other is not continuous, NextGENe highlights portions of the reads that align across the segment breakpoint. Typically, one end of the read matches to the end of one of the segments and the other end of the read is then mapped to the following segment, usually with low matching. The portion of the read that matches poorly is shown in lowercase with a gray background.