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Example sentences for: tsdfinder

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1); in this way, we dealt primarily with young L1 elements [ 23 ] . The TSDfinder program [ 23 37 38 ] was run on the RepeatMasker *.out output files in order to find the TSDs of the L1 elements, thereby refining the L1 boundaries.
The range of poly (A) tail lengths found by TSDfinder was 10-85 nucleotides.
This finding, combined with generally high TSD scores and manual inspection of hundreds of L1s recovered, gives us confidence that the sequences identified by the TSDfinder algorithm represent actual TSDs.
Finally, we observed that for two of the L1-TDs that do not have a polyadenylation signal, the sequence that the TSDfinder program defined as the poly(A) tail is 'patterned'; that is, the tail is composed of A-rich simple repeats (for example, AAATAAAT.
As seen in Figure 2, the majority of TSDs identified by TSDfinder had high TSD scores (the scoring system is described in Materials and methods), with an average score of 117 out of a maximum possible score of 140.