TABLE 2.
Primer sequences and amplification efficiencies of microsatellite and minisatellite loci selected for evaluations
| Locus | Trace | Targeted repeat(s)a | Primer sequence (5′-3′) | Annealing temp (°C) | Expected size (bp) | Amplification efficiency (no. of amplified samples/total no. of samples)b |
|---|---|---|---|---|---|---|
| CM-MS1 | 1649410765 | (GAACGAGATAGG)15 | ACCATCTAGAGATAACGAGCGA (F1) | 55 | 550 | 8/9 |
| GAATCAGAAGATGAGCGACAA (R1) | ||||||
| CGTGATAGTGGGTATGAATTGGACA (F2) | 55 | |||||
| CGACTGCGATACTCACGTCCT (R2) | ||||||
| CM-MS2 (HSP90) | 1649411347 | (CCATATCCC)6 | TTGCAACTGTACCTAAATTAGTA (F1) | 55 | 457 | 7/9 |
| GTGAGACTTCTGGGGTCCTGA (R1) | ||||||
| TCATGACGCGTCATACCAACA (F2) | 52 | |||||
| ACTTAGACAGTTCTATGCTGA (R2) | ||||||
| CM-MS3 | 1649411585 | (TGTTGG)9 and (GCTGCA)6 | AACCAAGTGAATCACGAACTT (F1) | 55 | 536 | 4/9 |
| TTGCTTTAAGTGTAGAGCATACAA (R1) | ||||||
| TCAAGTACAGCAGTCTATTGCTT (R1r) | ||||||
| GCAATATCTTCGACGATCCCA (F2) | 55 | |||||
| ATGGGAATAATTCTTCATCATCAA (R2) | ||||||
| CM-MS4 | 1649411639 | (ATC)73 | GTTGGCTGCATCTATGTT (F1) | 48 | 676 | 2/9 |
| TATACTTGATGATGTACTGGAT (R1) | ||||||
| TGTGGTGGAGTTGTAATTAGGA (F2) | 55 | |||||
| TAGATGGTGACTCAGATTCTT (R2) | ||||||
| CM-MS6 | 1649411735 | (AATGCAGATACAAGTATC)11 | TCTCTTTCCAACTCGATGCTT (F1) | 55 | 751 | 4/9 (weak bands) |
| ACCAAGAGTGATATTCATTCCTCT (R1) | ||||||
| GACTTACAATCAGATGGATACAGC (F2) | 58 | |||||
| TCTGTTCCTTGGTAAGTGGGCTGT (R2) | ||||||
| CM-MS8 | 1649411889 | (AT)44 | GCAACGTGACATGGATGGA (F1) | 52 | 307 | 0/7 |
| CGCTAGAGTCAAGAGTCAT (R1) | ||||||
| TTGTGGAGATAAATTAACAAACA (F2) | 52 | |||||
| CTCATCATCTGAAGTTGACAA (R2) | ||||||
| CM-MS11 | 1649412113 | (AT)21 | AGTCTTCATCATCTGGATATAGCA (F1) | 55 | 467 | 2/9 |
| GCTTTAGATTCTCGTACTATCA (R1) | ||||||
| ATCTAGAACAGTTCCCATTACCA (F2) | 52 | |||||
| AATGATGTCGAGTTAGCTAAA (R2) | ||||||
| CM-MS12 | 1649412180 | (TTTATTTT)6 | CTTGAAGGTTTAGAACCGGGA (F1) | 52 | 450 | 6/9c |
| (intergenic) | TTCGTGAAGGTACTTCATATG (R1) | |||||
| GGATCAATCCAAGTGAGTTCT (F2) | 55 | |||||
| CTCACATTGATATGGCTGGTT (R2) | ||||||
| CM-MS13 | 1649412266 | (TA)21 | GGACCACATGATAAAGAGCCA (F1) | 55 | 579 | 0/9 |
| TTGCGCTCTTGGGAAAGGTT (R1) | ||||||
| GACTTAGCAGATATAACTGGT (F2) | 52 | |||||
| CTCGCGCATGCATCAATGCAA (R2) | ||||||
| CM-MS14 | 1649412309 | (GTAGTAGTT)7 and (GTTGTAGTAGTA)11 | GTACCATCAGCTCCTATAGGA (F1) | 55 | 764 | 0/9 |
| GATCTGGCAGATCCAATTCAT (R1) | ||||||
| GGATCTTGCCAAATCACTTCT (F2) | 55 | |||||
| CTATCCTATAAGAGGTGATGTACT (R2) | ||||||
| CM-MS16 | 1649412803 | (CTTCTTCAT)9 | GAAGAGGTCGAAGTTAAGCTA (F1) | 50 | 597 | 7/9 |
| GACAATCATCTAAATCGTGTT (R1) | ||||||
| AAGTTTCATCTAGGTACACTAAGA (F2) | 55 | |||||
| CACTACCTAATCTCGTGTACTT (R2) | ||||||
| CM-MS17 | 1649413150 | (CTCGTTCCCTAT)15 | TCACTTGACTGCGATCTC (F1) | 50 | 532 | 2/9 |
| GTTCTTCAAGGTCCAGATCTCCTT (R1) | ||||||
| TACCCTAAGGAATAACGATCA (F2) | 52 | |||||
| ATGAGAAGTATCGCTCTTATGGCT (R2) | ||||||
| CM-MS18 | 1649412657 | (TA)15 | AGAGCCATCAGTACCACTGTT (F1) | 55 | 590 | 8/9c |
| TCGATTGGCCTTACCGGTGCA (R1) | ||||||
| CAGCTGTTCCAGAACCACTTGA (F2) | 55 | |||||
| CCAACAGACATAGACATGCTT (R2) |
a
Tandem repeat identified in the sequence of the C. muris whole-genome sequencing project.
b
Seven C. muris specimens (specimens 6853, 7379, 9412, 14260, 14272, 14713, and 14714) and two C. andersoni specimens (specimens 1808 and 11084) were used in initial primer evaluations. Specimens 9412 (except for MS1 and MM16) and 14272 (except for MS18) were not amplified at most loci.
c
Noisy at sequencing.