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Structure of an example alignment for a MER57F#LTR/ERV1 TE (marker Euarch187). The presence of the TE is shown in green and indicated by (+). The absence state is displayed in yellow and indicated by (−). TSD indicates the TE-flanking tandem sequence duplications that appear during the insertion process of elements and are hallmarks of orthology. The stringencies of selecting a diagnostic position are given below the sequences.
