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Fig. 3 | Mobile DNA

Fig. 3

From: CAULIFINDER: a pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes

Fig. 3

Overview of the multiple sequence alignments obtained for the VvinAV-VvinBV cluster using CAULIFINDER Branch A. The alignments were obtained using MAFFT with the ginsi and leave gappy regions 0.8 settings and visualized in the overview window of the Jalview program [39] with the following nucleotide colours: A (green), T (blue), G (red), C (orange). The colour densities are smoothed in the overview. The reference sequences are highlighted in red (VvinAV), blue (VvinBV_compA) or turquoise (VvinBV_compB). Branch A output sequences are not highlighted and concatemers have been removed for the ease of visualization. The raw alignments can be visualized in Supplementary Fig. 1. The alignments correspond to run 1 (A), run 2 (B) and run 3 (C). For the latter, only the VvinBV_compB sequences are shown

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Mobile DNA

ISSN: 1759-8753