Identification of possible loci of variable number of tandem repeats in Mycobacterium tuberculosis.

Three VNTR loci were previously cloned from Mycobacterium tuberculosis in our laboratory. The VNTR sequences were used as queries to search for similar sequences in the GenBank database by the BLAST program. Direct and tandem repeats were identified visually. The search revealed 45 more loci of direct and tandem repeats. Comparison of the sequences to the ones in the genome sequence database of the M. tuberculosis CDC1551 strain revealed 22 different loci. Combining these results with previously reported experimental work, at least 24 loci should be polymorphic enough to be detected by simple PCR. The repeats are present both inside coding sequences and in intergenic regions on the 5' or 3' ends of genes. M. tuberculosis contains several VNTR. Studies of their functions may be useful for understanding the differences of phenotypes between strains.