Fig. 3.

Expression of Copia-35 profiled with long reads. a) Long reads alignment of Cvi0-Copia35-15. Blue reads indicate matching orientation to the TE annotation (sense). b) Read depth of Cvi0-Copia35-15 in RNA-Seq data. c) TRALA plot of nine full-length Copia-35 copies. d) Alignment of full-length Copia-35 copies in Col-0, Ler-1, and Cvi-0. LTR boundaries are marked by yellow triangles. Col-0 copies are numbered 1 to 3; numbers on sequences of other accessions correspond to these Col-0 copies conserved among accessions. The Cvi-0 TIP is labeled as copy no. 4.