Skip to main content

Advertisement

Table 3 MLVA loci characteristics

From: Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping

Chromosome VNTR Locus Name Array start position in K96243 Consensus Repeat sequence In CDS Array Size in K96243 (bpxcopy#) Amplicon Size Range (bp) Number of Alleles Nei's Diversity
Large 933 k 933861 CGGCGAGGGAAA no 12 × 10 160–365 16 0.89
Small 2065 k 2064726 TCGAGTCA no 8 × 8 238–370 21 0.9
Large 2971 k 2971247 CGTGCTT no 7 × 9 201–314 22 0.92
Large 3145 k 3144932 CCTTCCTCG no 9 × 8 220–345 14 0.86
Large 2666 k 2666129 CTTTCGCTA yes 9 × 7 268–332 8 0.79
Large 3671 k 3671327 CTTGGAC no 7 × 21 205–364 23 0.93
Small 2115 k 2115424 CGCCGGTT no 8 × 15d 290–399 15 0.83
Large 2341 k 2340566 TTCGTGCGC no 9 × 7 122–219 10 0.8
Large 1500 k 1500968 GGGAAAGTGCG no 11 × 6 312–379 7 0.55
Small 3091 k 3091444 TCACGGC no 7 × 12 202–287 11 0.86
Large 3152 k 3152382 GACTCG no 6 × 17 160–371 26 0.94
Large 3652 k 3651903 CCGTAGTC no 8 × 8 320–408 13 0.87
Large 3564 k 3563188 GCAGCCTTCTTCGCG yes 15 × 30d 295–692 10 0.63
Large 20 k 20292 CGCCTCA no 7 × 10 245–435 22 0.92
Small 857 k 857207 CGAAYGAGC no 9 × 11 209–300 12 0.81
Small 1690 k 1689945 CGTCGATA no 8 × 13 252–405 13 0.78
Small 2445 k 2444540 GGCACTTC no 8 × 19 205–391 19 0.89
Small 1367 k 1366924 CGCRTCGAA yes 9 × 24 454–686 26 0.92
Small 1764 k 1764166 GCCGCTGAAGTT no 12 × 20 233–466 12 0.47
Large 2815 k 2815153 TGGCGTCTT yes 9 × 7 223–439 19 0.86
Large 2170 k 2171435 ATGCCGTGG no 9 × 24 229–513 25 0.93
Small 389 k 388768 GACGAACC no 8 × 6 224–313 12 0.87
Small 1788 k 1788368 GTCGTGCGATCCTGCT no 16 × 8 203–367 11 0.86
Large 1217 k 1217379 CGGACCTAGG no 10 × 15 357–480 14 0.85
Small 397 k 397146 GCCCGAGA no 8 × 12 226–401 17 0.88
Small 2050 k 2049749 CGATGCGGT/GCACCCAAC yes/yes 9 × 8/9 × 8 377–549 18 0.92
Small 2862 k 2861834 CTCGCCTTTG no 10 × 8 273–422 15 0.88
Large 140 k 139952 GCGCCGAA no 8 × 15 367–675 28 0.93
Large 2356 k 2356018 CTTGGCGA no 8 × 13 236–425 16 0.9
Small 2518 k 2517929 CCGCGAT no 7 × 31 294–394 17 0.92
Small 2124 k 2123866 CCTTCGCG no 8 × 23 332–490 14 0.88
Small 1934 k 1933513 CGAGTCGGCGGTT no 13 × 16 224–645 21 0.91