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Table 4 Summary of Tandem Repeats Finder (TRF) analysis.

From: Tandem repeat markers as novel diagnostic tools for high resolution fingerprinting of Wolbachia

Strain genome size TR TR size in total (% genome) mean TR period size (range) mean number of repeats/TR (range) mean TR internal match (%)
w Mel 1,267,812bp 93 20,349bp (1.6%) 80.9bp (10-291) 2.7 (1.8-11.8) 88.3
w Ri 1,445,904bp 94 16,667bp (1.1%) 58.5bp (10-378) 2.8 (1.8-8.8) 87.5
w Pip 1,482,530bp 72 13,268bp (0.9%) 68.5bp (12-399) 2.8 (1.8-10.6) 87.9
w Bm 1,080,114bp 11 1,032bp (0.1%) 42.8bp (3-112) 3.3 (1.9-15.7) 89.0
A. m. 1,197,687bp 54 8,541bp (0.7%) 64.4bp (11-495) 2.8 (1.9-11.2) 91.1
E. r. 1,516,355bp 201 95,290bp (6.3%) 138.7bp (1-471) 4.8 (1.8-65.1) 91.6
N. r. 879,977bp 27 5,569bp (0.6%) 68.8bp (9-297) 2.9 (1.9-4.9) 88.4
E. coli 4,649,675bp 89 17,807bp (0.38%) 70.4bp (8-304) 3.1 (1.9-12.5) 90.1
  1. Analysis in basic TRF basic mode included four completed Wolbachia genomes with strain names in bold, wMel (NCBI accession NC_002978), wRi (NC_012416), wPip (NC_010981) and wBm (NC_006833), and the genomes of Anaplasma marginale (A.m.) strain St. Maries (CP_000030), Ehrlichia ruminantium (E.r.) st. Welgevonden (NC_005295), Neorickettsia risticii (N.r.) st. Illinois (NC_013009) and Escherichia coli (E. coli) K12 substrain MG1655 (NC_000913). TRF detected several tandem repeats (TR) within the same genomic regions, as some tandem repeats contain internal repeats; the number of tandem repeats in column three does hence overrepresent the number of tandem repeat loci in the genome.