Markers + reference

Valeriana

8 species · Caprifoliaceae · Dipsacales

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Species 8
Genome length 155–157 kb
Candidate markers 268
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rbcL-accD LSC 704 0.0618 0.98 74.4 yes View details
accD LSC 1737 0.0646 0.90 76.3 yes View details
trnN-GUU-trnL-UAG IRb 1296 0.2162 0.88 70.4 yes View details
ycf1 SSC 5472 0.0704 0.99 78.0 yes View details
trnL-UAG-trnN-GUU IRa 1296 0.1587 0.82 68.8 yes View details
trnE-UUC-trnT-GGU LSC 933 0.0400 0.98 78.3 yes View details
ndhF-ndhD SSC 320 0.0722 0.97 70.5 yes View details
ndhG-ndhI SSC 365 0.0576 1.00 70.3 yes View details
atpF-atpH LSC 392 0.0449 1.00 69.8 yes View details
accD-psaI LSC 580 0.0375 0.99 69.2 yes View details
trnK-UUU-rps16 LSC 564 0.0375 1.00 69.1 yes View details
pafII-cemA LSC 429 0.0424 1.00 68.7 yes View details
infA-rps8 LSC 111 0.0706 0.99 68.7 yes View details
rpl22-rps19 LSC 91 0.0651 0.99 68.6 yes View details
ndhC-trnV-UAC LSC 723 0.0435 1.00 68.5 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCGGTCTTCAAAACTT AAGGAGGGCAGAGGTTTTTG 741–788 0.875 82.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACTCGTGGAAAAACCCTTCC AAGGAGGGCAGAGGTTTTTG 1044–1091 0.875 81.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 ACTCGTGGAAAAACCCTTCC TGCCGAAGAGAAGGAAGAGA 1181–1228 0.875 80.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 ACTCGTGGAAAAACCCTTCC CCACAGTGTATCACGCAAGA 1729 0.250 49.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 ACTCGTGGAAAAACCCTTCC TCCACAGTGTATCACGCAAG 1730 0.250 49.2
atpF-atpH_p1 atpF-atpH AGAAAGAGTACCATGCTGCG GCTGTAGAAGGTATCGCGAG 907–941 1.000 87.2
atpF-atpH_p2 atpF-atpH AGAAAGAGTACCATGCTGCG TGATTTCTGCTGCTTCCGTT 999–1033 1.000 86.3
atpF-atpH_p3 atpF-atpH AGGAAAAAGTACAGCTGGGC GCTGTAGAAGGTATCGCGAG 715–749 0.875 82.4
atpF-atpH_p4 atpF-atpH CAATACCCCGAGCACTACAC GCTGTAGAAGGTATCGCGAG 656–672 0.875 78.7
atpF-atpH_p5 atpF-atpH AGAAAGAGTACCATGCTGCG TTGTGCGTTGCGTTGAATTT 1319–1342 0.625 67.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 959–1041 1.000 90.3
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 957–1039 1.000 90.3
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA TGGCGTTACTCTACCACTGA 956–1038 1.000 90.1
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA TGGCGTTACTCTACCACTGA 954–1036 1.000 90.1
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GATGTCCTGAACCGCTAGAC CCATGGCGTTACTCTACCAC 956–1038 1.000 89.8
ndhC-trnV-UAC_p1 ndhC-trnV-UAC TCAATGAAGCAACAGCTGGT AGCCTGACAAATGGTTTGGT 1789–1988 1.000 86.3
ndhC-trnV-UAC_p2 ndhC-trnV-UAC AAGGGCAACTCAACGGAATT AGCCTGACAAATGGTTTGGT 1672–1881 1.000 86.2
ndhC-trnV-UAC_p3 ndhC-trnV-UAC CTAAGACCATTCCAAGGCCC AGCCTGACAAATGGTTTGGT 1601–1810 1.000 85.9
ndhC-trnV-UAC_p4 ndhC-trnV-UAC AAGGGCAACTCAACGGAATT ATGGTTTGGTCCGAATCAGG 1662–1861 0.750 74.8
ndhC-trnV-UAC_p5 ndhC-trnV-UAC TCAATGAAGCAACAGCTGGT ATGGTTTGGTCCGAATCAGG 1779–1978 0.750 74.6
rbcL-accD_p1 rbcL-accD TTGAATGCTACTGCGGGTAC AAACCAGACAAACTCGTGCT 1548–1567 0.625 69.0
rbcL-accD_p2 rbcL-accD TTGAATGCTACTGCGGGTAC AACCAGACAAACTCGTGCTT 1547–1566 0.625 68.9
rbcL-accD_p3 rbcL-accD ATGAAATTATCCGTGCGGCT TCTTTGTGCGAAACCAGACA 951–970 0.375 58.7
rbcL-accD_p4 rbcL-accD AATGAGGGACGTGATCTTGC TCTTTGTGCGAAACCAGACA 982–1001 0.375 58.6
rbcL-accD_p5 rbcL-accD TTGAATGCTACTGCGGGTAC TCTTTGTGCGAAACCAGACA 1558–1577 0.375 57.3
accD_p1 accD TGGGCTAGATGGAGGTCAAA CCAACAGCGATTCTGAGTCA 1989–2274 0.500 66.8
accD_p2 accD TTGGGCTAGATGGAGGTCAA CCAACAGCGATTCTGAGTCA 1990–2275 0.500 66.8
accD_p3 accD TTTGGGCTAGATGGAGGTCA CCAACAGCGATTCTGAGTCA 1991–2276 0.500 66.8
accD_p4 accD TGGGCTAGATGGAGGTCAAA AAGAAGCCATTGCAATTGCC 2396–2690 0.500 66.3
accD_p5 accD TTGGGCTAGATGGAGGTCAA AAGAAGCCATTGCAATTGCC 2397–2691 0.500 66.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Valeriana dageletiana PQ280047.1 155311 View on NCBI ↗
Valeriana dioica PP316498.1 155234 View on NCBI ↗
Valeriana fauriei NC_065841.1 155302 View on NCBI ↗
Valeriana flaccidissima PP056254.1 155113 View on NCBI ↗
Valeriana jatamansi NC_067975.1 155138 View on NCBI ↗
Valeriana montana PP316499.1 154581 View on NCBI ↗
Valeriana saxatilis PP190937.1 156689 View on NCBI ↗
Valeriana tripteris PP316501.1 154832 View on NCBI ↗