Figure 2

Screenshot of the LTRsift main window. (a) Putative family list, (b) candidate list, (c) candidate details, (d) candidate visualization. The currently loaded project contains 13,943 candidates from the Monodelphis domestica genome, with the currently selected candidate showing a full set of detected features (PBS, PPT, protein domains). ORF detection and reference matching have been performed. Additional details, such as PPT and PBS sequences, Pfam IDs and so on, are available by scrolling to the right in (c). The graphical representation in (d) depicts the retrotransposon (red) with PPT and PBS as small lines in the two tracks below. The next track shows protein domain matches, coded in different colors. Here integrase domains are depicted in blue, reverse transcriptase domains in red, protease domains in purple, RNase H domains in gold, and any other domains in green. The RNase H domain is marked in red because it has been selected in the candidate detail list. The reference match in the track below (shown in yellow) spans the interior region of the candidate completely, suggesting that it likely is a full-length element. The bottom track shows open reading frames in blue color. LTR: long terminal repeat; ORF: open reading frame; PBS: primer binding site; PPT: polypurine tract; TSD: target site duplication.