This track shows the position of gaps -- represented by Ns -- within the C. intestinalis assembly. Gaps of 50 or more bases were most likely introduced by the JGI JAZZ assembler.
For a discussion of gaps and the JAZZ assembler see The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins (Supplemental Materials). Science. 2002 Dec 13;298(5601):2157-67.