Markers + reference

Hepatica

9 species · Ranunculaceae · Ranunculales

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Species 9
Genome length 159–161 kb
Candidate markers 279
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 279 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 746 0.0067 1.00 52.6 yes View details
trnK-UUU-psbA LSC 346 0.0179 0.93 59.6 yes View details
ycf3-psaA LSC 732 0.0101 0.98 48.7 yes View details
trnT-GGU-trnE-UUC LSC 713 0.0124 0.98 62.0 yes View details
atpH-atpF LSC 452 0.0175 0.96 57.6 yes View details
trnG-GCC-trnS-GCU LSC 1636 0.0069 1.00 61.0 yes View details
ndhC-trnV-UAC LSC 922 0.0133 1.00 62.7 yes View details
petA-psbJ LSC 438 0.0156 1.00 68.2 yes View details
ycf1 IRb 1658 0.0027 1.00 36.4 no View details
ndhF SSC 2196 0.0082 0.99 45.6 yes View details
ndhF-trnL-UAG SSC 1406 0.0097 0.98 63.9 yes View details
ccsA-ndhD SSC 278 0.0714 0.96 72.7 yes View details
ycf1 SSC 5655 0.0050 0.99 44.1 yes View details
ycf1-ndhF SSC 87 0.3975 0.97 72.3 yes View details
ndhD-psaC SSC 147 0.0354 1.00 69.0 yes View details
trnG-UCC-psbZ LSC 371 0.0154 0.99 66.0 yes View details
ndhG-ndhI SSC 160 0.0207 1.00 65.2 yes View details
trnL-UAA-trnF-GAA LSC 180 0.0153 1.00 64.5 yes View details
psbD-trnT-GGU LSC 1361 0.0051 0.99 62.7 yes View details
rps16-trnK-UUU LSC 673 0.0068 1.00 62.6 yes View details
psbM-petN LSC 1012 0.0054 0.99 61.6 yes View details
ndhE-ndhG SSC 265 0.0188 0.97 61.2 yes View details
trnD-GUC-psbM LSC 1122 0.0044 1.00 59.3 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 TACCCTCCCTTTTGTTTGGC ATTGGATTGCACAACCCCAT 1861–1995 1.000 85.7
rps16_p2 rps16 TACCCTCCCTTTTGTTTGGC TGTGTTGGATTGGCACTTCA 1448–1580 1.000 85.5
rps16_p3 rps16 ATCTCCCCGTGAAGAATTGC ATTGGATTGCACAACCCCAT 2044–2178 1.000 85.2
rps16_p4 rps16 ATCTCCCCGTGAAGAATTGC TGTGTTGGATTGGCACTTCA 1631–1763 1.000 85.0
rps16_p5 rps16 TACCCTCCCTTTTGTTTGGC ACTTGTGTTGGATTGGCACT 1451–1583 0.889 80.4
rps16-trnK-UUU_p1 rps16-trnK-UUU ATGAAATGCCAAGGACTCGG AAAGCCGAGTACTCTACCGT 788–866 1.000 82.6
rps16-trnK-UUU_p2 rps16-trnK-UUU ATGAAATGCCAAGGACTCGG AAGCCGAGTACTCTACCGTT 787–865 1.000 82.6
rps16-trnK-UUU_p3 rps16-trnK-UUU ATGAAATGCCAAGGACTCGG TCTACCAACGGTATGGACGA 853–931 1.000 82.5
rps16-trnK-UUU_p4 rps16-trnK-UUU CCAAGGACTCGGGATTTTCC TCTACCAACGGTATGGACGA 845–923 1.000 82.5
rps16-trnK-UUU_p5 rps16-trnK-UUU CCAAGGACTCGGGATTTTCC AAGCCGAGTACTCTACCGTT 779–857 1.000 82.5
trnK-UUU-psbA_p1 trnK-UUU-psbA ACTCCATCCGACTAGTTCCG TCGCGTCTCTCTAAAATTGCA 243–414 1.000 74.3
trnK-UUU-psbA_p2 trnK-UUU-psbA ACTCCATCCGACTAGTTCCG TACCCAGTTACAGAAGCGAC 280–451 1.000 74.2
trnK-UUU-psbA_p3 trnK-UUU-psbA ACTCCATCCGACTAGTTCCG CAGTTACAGAAGCGACCCC 276–447 1.000 73.3
trnK-UUU-psbA_p4 trnK-UUU-psbA ACTCCATCCGACTAGTTCCG CCAGTTACAGAAGCGACCC 277–448 1.000 73.3
trnK-UUU-psbA_p5 trnK-UUU-psbA ACTCCATCCGACTAGTTCCG CCCAGTTACAGAAGCGACC 278–449 1.000 73.3
ycf3-psaA_p1 ycf3-psaA TGAAATTGCAGAGGCTTGGT ATGCCACTCAGCCAAAGAAA 1094–1128 1.000 84.0
ycf3-psaA_p2 ycf3-psaA TGAAATTGCAGAGGCTTGGT TGCCACTCAGCCAAAGAAAT 1093–1127 1.000 84.0
ycf3-psaA_p3 ycf3-psaA TGAAATTGCAGAGGCTTGGT TAATGGAACCAACCGGCAAA 1364–1398 1.000 83.2
ycf3-psaA_p4 ycf3-psaA GTTAGAGGAAGCGCCGTAAA ATGCCACTCAGCCAAAGAAA 1651–1689 1.000 82.8
ycf3-psaA_p5 ycf3-psaA GTTAGAGGAAGCGCCGTAAA TGCCACTCAGCCAAAGAAAT 1650–1688 1.000 82.8
trnG-UCC-psbZ_p1 trnG-UCC-psbZ AATCGAACCCGCATCTTCTC TTGCTTCTTCTGACGGTTGG 517–627 1.000 82.4
trnG-UCC-psbZ_p2 trnG-UCC-psbZ GAATCGAACCCGCATCTTCT TTGCTTCTTCTGACGGTTGG 518–628 1.000 82.4
trnG-UCC-psbZ_p3 trnG-UCC-psbZ AATCGAACCCGCATCTTCTC GCTTCTTCTGACGGTTGGTC 515–625 1.000 78.9
trnG-UCC-psbZ_p4 trnG-UCC-psbZ GAATCGAACCCGCATCTTCT GCTTCTTCTGACGGTTGGTC 516–626 1.000 78.9
trnG-UCC-psbZ_p5 trnG-UCC-psbZ GAACCCGCATCTTCTCCTTG TTGCTTCTTCTGACGGTTGG 513–623 1.000 77.9
psbD-trnT-GGU_p1 psbD-trnT-GGU TCTCCGTAACCAGTCATCCA GCCCTTTTAACTCAGCGGTA 1408–1535 1.000 82.7
psbD-trnT-GGU_p2 psbD-trnT-GGU TCTCCGTAACCAGTCATCCA GGCGTAAGTCATCGGTTCAA 1371–1498 1.000 81.3
psbD-trnT-GGU_p3 psbD-trnT-GGU GGTCTCTCCGTAACCAGTCA GCCCTTTTAACTCAGCGGTA 1412–1539 1.000 80.8
psbD-trnT-GGU_p4 psbD-trnT-GGU TCTCCGTAACCAGTCATCCA TAGGCCCTTTTAACTCAGCG 1411–1538 1.000 80.3
psbD-trnT-GGU_p5 psbD-trnT-GGU GGTCTCTCCGTAACCAGTCA GGCGTAAGTCATCGGTTCAA 1375–1502 1.000 79.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Hepatica acutiloba NC_060983.1 159497 View on NCBI ↗
Hepatica americana NC_060984.1 159805 View on NCBI ↗
Hepatica asiatica NC_045910.1 160157 View on NCBI ↗
Hepatica falconeri NC_060985.1 161075 View on NCBI ↗
Hepatica insularis NC_062086.1 160377 View on NCBI ↗
Hepatica maxima NC_045909.1 160876 View on NCBI ↗
Hepatica nobilis NC_060986.1 160635 View on NCBI ↗
Hepatica nobilis var. japonica NC_045878.1 160988 View on NCBI ↗
Hepatica transsilvanica NC_060987.1 161005 View on NCBI ↗