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Additional file 3: Detailed table of repeats found.
See Table 2 for the first few lines of the table of repeats for chromosome 1 of Homo sapiens.
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The genome-wide table of tandem repeats identified by the Tandem Repeat Finder program [ 39] was reduced to the set of highly pure STRs by filtering for TRs with a length less than or equal to 9 bp and repeat purity of at least 90%.
Finally, the repeat content of the genome was reduced to a table of merged repeat lengths and the number of times they were observed.
Additional file 2: Table of found repeated sequences.
A count table of the repeat families is also included in Supplementary file 1B.
Indeed, as noted in the genotyping analysis, there were 3 predominant PFGE clones that belonged to 2 genetic lineages and accounted for the majority (98.2%, Table 3) of repeated MRSA infections in this children's hospital.
In order to address concerns related to possible lower levels of effort exerted by some individuals in their senior year; the second set of columns of Table 6 repeats the analysis but uses changes between the freshman and junior year.
A number of different flanklength, mismatch and hit retention parameters were evaluated and the results were compared to both the results of Denoeud and Vergnaud and to the original dataset of repeats detected (Table 1, Table 2).
These TEs within DANGER genes are likely the result of recent independent transpositions, since orthologous genetic regions contain different classes of repeats (table S2).
The amplified DNA was cloned using the TopoTA kit (Invitrogen), and individual clones were sequenced and analyzed for the presence of repeats (Table 1).
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