De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis
CDSs, introns, and regions upstream of CDSs (in 1 kb steps ranging from 1 to 4 kb) were used for comparison. Only those upstream regions were used that do not overlap with a protein coding region. Each region was used only once even if it is upstream of two divergently transcribed genes to avoid double-counting. The box plots show the distribution of % pairwise identities with the median value as a horizontal line in the box between the first and third quartiles. Detailed information on the comparisons can be found in Figure S4 and Table S5.