SCPEP1 consistent mRNA alignments. Screenshots taken from the NCBI Sequence Viewer displaying the gene model for serine carboxypeptidase 1 (SCPEP1) where green bars represent contigs and mRNA alignments are shown with red bars as alignments to exons. (a) Contig31.166 contains three putative exons. However, it overlaps neighboring Contig31.165 for all of its length (7,162 bp) at 98.6% identity, and mate pairs indicate that the two contigs came from the same position. Every mRNA alignment takes a path through the exons such that only one copy of each duplicated exon is included. (b) When the contig is moved, the extra copies of these three apparently duplicated exons are removed, but all of the alignments remain consistent.