Selection procedure of minisatellites for Y. pestis 3A: Sixty-four tandem repeats have at least 7 units longer than 9 base-pairs. Panel A presents the distribution of these 64 loci according to repeat unit length. Each rectangle is an hyperlink to an alignment file. The rectangle indicated by the arrow is linked to the file illustrated in panel B. 3B: This is an annotated alignment file. The file corresponds to Yp3057ms09 (Table 1 and Figure 4; Yp : Yersinia pestis; 3057 : position on the genome, expressed in kilobases; MS09 : MiniSatellite index). The consensus pattern of 18 base-pairs is aligned to each motif. Annotations of the file are inserted within brackets. Although this minisatellite is very polymorphic, eleven different motifs (labeled a-k) are observed in the sequenced allele. The first four and last two copies are most diverged and rare. Four types of motifs (f, g, h, i) constitute most of the array. For convenience, 18 motifs have been removed from the alignment file and replaced by their letter code. The last two copies are 21 base-pair long instead of 18. The end of the alignment file (panel B, bottom) provides sequence data flanking the tandem repeat array. The positions of the primers chosen for PCR amplification of this locus (Table 1) are shown underlined.
Le Flèche et al. BMC Microbiology 2001 1:2 doi:10.1186/1471-2180-1-2