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Fig. 9 | Mobile DNA

Fig. 9

From: Look4LTRs: a Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats

Fig. 9

The castle problem. Represented are two LTR-retrotransposons of the same family. For simplicity, the internal parts were ignored. The first element is colored blue (vertical hatching pattern) and the second element is colored yellow (horizontal hatching pattern). In this case, a singular vector of scores was used where positive y-values mark a distance to a matching k-mer in the forward direction and negative y-values mark a distance to a matching k-mer in the backward direction. Only the closest match is scored, regardless of direction. The 5’ LTR of the left element is clearly distinguished. The 3’ LTR of the left element is broken into positive and negative scores. The same holds for the 5’ LTR of the right element. The 3’ LTR of the right element is clearly distinguished. In essence, the castle problem is where the scores of the LTRs become fragmented as a result of nearby, same-family elements

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