Fig. 4: TEtrimmer provides comprehensive report plots for each discovered TE.

The B. hordei LTR retrotransposon named ltr-1-family-22, initially annotated by RepeatModeler2 and re-analyzed with TEtrimmer, is shown as an example (consensus sequences: Source data file). A The alignment of 33 sequences in total shows the TE boundary regions of the MSA (100 nucleotide sites are displayed for each side) after TEtrimmer analysis. Nucleotide background colors (A, green; C, blue; G, black; T, red) in the MSA represent sites where the proportion of the respective nucleotide is below 0.4. The TE boundaries defined by TEtrimmer are indicated as TE start (red) and TE end (blue). The two boundary regions were artificially connected by ten gaps (-), and the total length of the MSA is indicated on the top. B The plot shows the entire MSA after TEtrimmer analysis. The TE boundaries are indicated as in (A). Nucleotides are represented with colored bars; gaps are indicated as blank regions in the plot. The x-axis gives the nucleotide position (in bp) within the MSA. C The panels show a BLASTN plot before (left panel) and after (right panel) TEtrimmer analysis. The x-axis indicates the TE consensus nucleotide position (in bp), and the y-axis is the sequence divergence in percent compared to the TE consensus sequence. Each line indicates a BLASTN hit; red lines highlight hits with a sequence divergence below 1.5% and a sequence coverage >90%. D Self-dot plots before (left panel) and after (right panel) TEtrimmer analysis. The axes show the nucleotide position (in bp) in the TE consensus sequence. E The plot shows a genomic map of open reading frames (ORFs; blue arrows) and PFAM domains (red arrows) predicted in the TE consensus sequence before (upper panel) and after (lower panel) TEtrimmer analysis. F Dot plots (window size = 25 bp, threshold = 50; the threshold represents the minimal sum of substitution scores in a defined window required for a dot to be plotted) of the TE consensus sequence before (y-axis) and after (x-axis) TEtrimmer analysis. Axes show the nucleotide position (in bp).