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As shown Fig. 3A, we observed a clear inverse correlation between the total number of repeats per genome and the number of prophages within each genome (R = −0.83; P<0.001).
Of the total number of repeats, fifty sequences (926 copies) appeared to be of phage origin.
The total number of nucleotides separating the embedded STR regions and the total number of repeats at the microsatellite locus were also tabulated.
The total number of repeats is lower than expected by chance; especially the number of mononucleotide repeats is significantly lower than expected (Tables 1 and 2).
Additionally, the total number of repeats, either ATTCTRTG or TTCTRTGA, in subfamily I was tallied and both octomer sequences occurred at equal frequencies.
For each microsatellite, all STR regions were identified in its ePCR fragment sequence and the total number of repeats was tabulated.
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The sum of all of these unresolved repeats is the total number of repeat-induced gaps in the assembly.
We plotted the proportion of SINE and LINE elements per random selected 100 Kb window and sorted them for their total number of repeat integrations, as we expected to find equal proportions to be more likely to occur at higher repeat numbers.
The total number of repeat types in each organism is reported in Figure 2.
Sample sizes are the total number of repeated observations across all 16 subjects.
Like REPuter, VMATCH identifies all overlapping repeated sequences and thus overestimates the total number of repeated elements in a genome.
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