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Example sentences for: tsd

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If the 5' HSP ends further away from L1 start, the score function is described by the formula: P × 80/(FF -10), where FF is the length of the L1 5'-flanking sequence used for TSD finding (100 nucleotides is default) and P is the 5' HSP end position within this flank.
The classification of an L1 insertion as an L1-TD was only allowed when a 3' TSD closer to the L1, indicating a standard insertion event, could not be found (see [ 23 37 38 ] ). The coordinates of the candidate transduced regions (the gi record and the begin and end coordinates) were stored for later analysis.
We manually inspected these sequences for the presence of either AATAAA or ATTAAA polyadenylation signals no more than 100 nucleotides upstream of the poly(A) tail that preceded the 3' TSD [ 43 ] . We were able to identify a polyadenylation signal in 11 of our 25 examples of 3' transduction events (Table 2and Figure 3a).
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.
The distribution of TSD lengths (Figure 2) correlates well with TSDs observed in biological experiments [ 12, 14, 34, 35].