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Table 2 List of primers, their sequences, amplification conditions and locus details

From: Isolation of Mycobacterium avium subspecies paratuberculosis from Ugandan cattle and strain differentiation using optimised DNA typing techniques

Primer name

Position on MAP K10 genome, acc. no AE016958

Sequence

Target

Thermal conditions (x = No. of cycles)

Reference

IS900/150 C

39946-39969

5´-CCGCTAATTGAGAGATGCGATTGG-3’

IS900

95 °C-3 min, 45x: 95 °C-30 sec,61 °C-30 sec; 72 °C-20 sec; 72 °C-3 min

[32]

IS900/921

40174-40150

5´-AATCAACTCCAGCAGCGCGGCCTCG-3’

MA901/373up

Not applicable

5’-CGGATTGCTAACCACGTGGTGTGTG-3’

IS901

95 °C-3 min, 45x: 95 °C-30 sec; 60 °C-30 sec; 72 °C-40 sec; 72 °C-3 min

[25]

MA901/956do

Not applicable

5’-GTGCTGCGAGTTGCTTGATGAG-3’

IS1311auF (M56)

33911- 33930

5’-GCGTGAGKCTCTGTGGTGAA-3’

IS1311

95 °C-3 min, 45x: 95 °C - 30 sec; 59 °C - 30 sec; 72 °C-40 sec; 72 °C-3 min

[11, 19] and this study

M119

33323-33340

5’-ATGACGACCGCTTGGGAG-3’

M2/F

3253559-3253583

5’-CCTGCTCGACGAACACCTCAA-3’

MIRU 2

95 °C-3 min, 47x: 97 °C-30 sec; 60 °C-30 sec; 72 °C-60 sec; 72 °C-3 min

This study

M2/R

3253860-3253834

5’-CGAAGATCCTGGGACTGGACGAGTTGG-3

M3/F

4441771-4441797

5’-CGGATCGACATTCACCCTGTCCATTCC-3’

MIRU 3

95 °C-3 min, 47x: 97 °C-30 sec; 57 °C-30 sec; 72 °C-60 sec; 72 °C-3 min

This study

M3/R

4442081-4442059

5’-CGAAGCCCTCCTTACGGAGCAGG-3’

M32/F

115702-1125726

5’-CAGCGCCACAGGGTTTTTGGTGAAG-3’

VNTR 32

95 °C-3 min, 47x: 97 °C-30 sec; 60 °C-30 sec; 72 °C-60 sec; 72 °C-3 min

This study

M32/R

1126006-1125981

5’-GCGGAAATCCAACAGCAAGGACGGAC-3’

SRL1F

1793439-1793420

5’- GGTGTTCGGCAAAGTCGTTGTGCC-3

SSR 1

95 °C-3 min, 47x: 97 °C-30 sec; 61 °C-30 sec; 72 °C-40 sec; 72 °C-3 min

This study

SRL1R

1792995-1793014

5’-GCGCGTCAGACTGTGCGGTATGG-3’

SRL2F

2719265-2719287

5’-CGGCTGCACTTGCACGACTCTAGG-3’

SSR 2

95 °C-3 min, 47x: 97 °C-30 sec; 64 °C-60 sec; 72 °C-40 sec; 72 °C-3 min

This study

SRL2R

2718879-2718902

5’-GCGTAGCGTTGTGGGCTTGGAGG-3’

SLR8F

1027929-1027950

5’-GCGAGATGTCGACCATCCTGAC-3’

SSR 8

95 °C-3 min, 47x: 97 °C-30 sec; 59 °C-30 sec; 72 °C-20 sec; 72 °C-3 min

This study

SLR8R

1028263-1028283

5’-CGCTCGACGATCAGCGTGTTG-3’

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