Markers + reference

Myrospermum

2 species · Fabaceae · Fabales

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Species 2
Genome length 164–168 kb
Candidate markers 264
Primer pairs 80

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5475 0.4104 0.84 74.5 yes View details
ndhH SSC 1182 0.4788 0.90 82.1 yes View details
ndhA SSC 2386 0.4706 0.85 78.9 yes View details
ndhG SSC 531 0.4267 0.87 80.2 yes View details
ndhD SSC 1500 0.4919 0.91 82.5 yes View details
ndhF SSC 2244 0.4728 0.89 81.0 yes View details
trnT-UGU-trnL-UAA LSC 1430 0.0891 0.92 88.8 yes View details
trnG-UCC-trnR-UCU LSC 451 0.1175 0.85 87.5 yes View details
ndhC-trnV-UAC LSC 1014 0.2236 0.95 87.5 yes View details
trnP-UGG-psaJ LSC 909 0.1021 0.93 87.4 yes View details
trnK-UUU-rps16 LSC 1780 0.1348 0.92 85.5 yes View details
psbZ-trnG-GCC LSC 600 0.1083 1.00 84.5 yes View details
rps11-rpl36 LSC 871 0.1539 0.93 83.8 yes View details
rps8-rpl14 LSC 737 0.1389 0.89 83.8 yes View details
ycf4-cemA LSC 480 0.0719 0.96 82.8 yes View details
trnL-UAG-rpl32 SSC 951 0.4125 0.89 82.0 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGCCGAGTACTCTACCATTGA AAGGCGGGTGTTTTTATGGA 1811–1866 1.000 81.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGCCGAGTACTCTACCATTGA AGGCGGGTGTTTTTATGGAA 1810–1865 1.000 81.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGCCGAGTACTCTACCATTGA GGCGGGTGTTTTTATGGAAC 1809–1864 1.000 81.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 GCCGAGTACTCTACCATTGAG AAGGCGGGTGTTTTTATGGA 1810–1865 1.000 78.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 GCCGAGTACTCTACCATTGAG AGGCGGGTGTTTTTATGGAA 1809–1864 1.000 78.8
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 491–531 1.000 74.4
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 494–534 1.000 74.1
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 497–537 1.000 73.6
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 500–540 1.000 73.4
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU ACCAAAGTTTCACGTTCGGT AGAAGACCTCTGTCCTATCCA 561–601 1.000 71.7
psbZ-trnG-GCC_p1 psbZ-trnG-GCC CTTCTCCTGATGGTTGGTCG CGTCTTCTCCTTGGCAAAGA 754–2450 1.000 81.8
psbZ-trnG-GCC_p2 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG CGTCTTCTCCTTGGCAAAGA 757–2453 1.000 80.2
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TCCTGATGGTTGGTCGAGTA CGTCTTCTCCTTGGCAAAGA 750–2446 1.000 80.1
psbZ-trnG-GCC_p4 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC CGTCTTCTCCTTGGCAAAGA 755–2451 1.000 79.8
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TTCTCCTGATGGTTGGTCGA CGTCTTCTCCTTGGCAAAGA 753–2449 1.000 79.0
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 1426–1480 1.000 89.3
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 1434–1488 1.000 88.8
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 1458–1512 1.000 88.3
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 1466–1520 1.000 87.8
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG AGTCCGTAGCGTCTACCAAT 1440–1494 1.000 87.4
ndhC-trnV-UAC_p1 ndhC-trnV-UAC GGCTCGATATTATTAGAAATGCCC AGAAGGTCTACGGTTCGAGT 1102–1329 1.000 54.7
ndhC-trnV-UAC_p2 ndhC-trnV-UAC GGCTCGATATTATTAGAAATGCCC GAAGGTCTACGGTTCGAGTC 1101–1328 1.000 51.9
ndhC-trnV-UAC_p3 ndhC-trnV-UAC GGCTCGATATTATTAGAAATGCCC GTTCGAGTCCGTATAGCCCT 1090–1317 1.000 51.2
ndhC-trnV-UAC_p4 ndhC-trnV-UAC GCTCGATATTATTAGAAATGCCCA AGAAGGTCTACGGTTCGAGT 1101–1328 1.000 51.2
ndhC-trnV-UAC_p5 ndhC-trnV-UAC GGCTCGATATTATTAGAAATGCCC AAGGTCTACGGTTCGAGTCC 1100–1327 1.000 51.2
ycf4-cemA_p1 ycf4-cemA TTGGCCTATTTCTTGCGTGT AATGCGAAAGAGATGCACCA 593–599 1.000 85.1
ycf4-cemA_p2 ycf4-cemA AAAAAGCTGCAGAATTGGCC AATGCGAAAGAGATGCACCA 607–613 1.000 84.3
ycf4-cemA_p3 ycf4-cemA AAAGCTGCAGAATTGGCCTA AATGCGAAAGAGATGCACCA 605–611 1.000 83.9
ycf4-cemA_p4 ycf4-cemA TTGGCCTATTTCTTGCGTGT GCACCAGGGCAAAAAGACTA 579–585 1.000 83.6
ycf4-cemA_p5 ycf4-cemA GCCATTCCCTTGACTCGTAC AATGCGAAAGAGATGCACCA 659–665 1.000 82.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Myrospermum frutescens PV870751.1 164247 View on NCBI ↗
Myrospermum sousanum NC_067515.1 168148 View on NCBI ↗