Markers + reference

Trollius

17 species · Ranunculaceae · Ranunculales

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Species 17
Genome length 160–161 kb
Candidate markers 271
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 307 0.0179 0.93 56.3 yes View details
trnK-UUU-rps16 LSC 699 0.0160 1.00 55.7 yes View details
rps16-trnQ-UUG LSC 1242 0.0104 0.97 60.2 yes View details
trnT-GGU-psbD LSC 1584 0.0062 1.00 52.8 yes View details
ndhC-trnV-UAC LSC 1521 0.0248 0.94 71.3 yes View details
ycf4-cemA LSC 833 0.0186 1.00 60.1 yes View details
ycf1 IRb 1089 0.0107 1.00 57.0 yes View details
ndhF SSC 2229 0.0058 1.00 39.8 yes View details
ndhF-rpl32 SSC 963 0.0134 1.00 71.2 yes View details
rpl32-trnL-UAG SSC 1027 0.0165 0.99 72.3 yes View details
ycf1 SSC 5343 0.0063 1.00 45.7 no View details
ycf1-ndhF SSC 49 0.2609 0.84 68.5 yes View details
psbT-psbN LSC 82 0.0405 0.94 65.6 yes View details
ndhH-rps15 SSC 141 0.0241 1.00 65.0 yes View details
trnT-UGU-trnL-UAA LSC 1396 0.0074 0.98 64.9 yes View details
ycf3-trnS-GGA LSC 896 0.0094 1.00 63.5 yes View details
rpl14-rpl16 LSC 143 0.0193 1.00 63.4 yes View details
psbE-petL LSC 1264 0.0080 0.98 62.7 yes View details
petA-psbJ LSC 378 0.0117 0.99 61.9 yes View details
rps19-trnH-GUG LSC 30 0.0505 1.00 59.3 no 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 382–425 1.000 87.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 396–439 1.000 87.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 395–438 1.000 87.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 397–440 1.000 87.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TATCATCAACCGCGCTAACC 393–436 1.000 86.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT CTTGAAAAAGGCGCTCAACC 905–1000 1.000 84.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT ATTCTTTCTCGAGCCGTACG 1112–1207 1.000 83.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCAGGGGATTTCTTGGG CCTTGAAAAAGGCGCTCAAC 1515–1610 1.000 82.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCAGGGGATTTCTTGGG CTTGAAAAAGGCGCTCAACC 1514–1609 1.000 82.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAAGCAGGGGATTTCTTGGG ATTCTTTCTCGAGCCGTACG 1721–1816 1.000 82.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCACAACCGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1308–1361 1.000 84.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1287–1340 1.000 83.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1298–1351 1.000 83.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAACCGATCATGTCCTT CTCGGAGGTTCGAATCCTTC 1312–1365 1.000 82.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1291–1344 1.000 82.8
trnT-GGU-psbD_p1 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA ACAAAAACGAAACGGTCCCT 1727–1772 1.000 81.0
trnT-GGU-psbD_p2 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA CAAAAACGAAACGGTCCCTC 1726–1771 1.000 79.8
trnT-GGU-psbD_p3 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA ACAAAAACGAAACGGTCCCT 1690–1735 1.000 79.7
trnT-GGU-psbD_p4 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA TCCCTCCGTAACCAGTCATC 1712–1757 1.000 78.9
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA CAAAAACGAAACGGTCCCTC 1689–1734 1.000 78.5
ycf3-trnS-GGA_p1 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA TGTTCGTGAATTAGGCGAGG 1004–1037 1.000 76.5
ycf3-trnS-GGA_p2 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA CCCTCGGTAAACAAAAGCCT 961–994 1.000 76.0
ycf3-trnS-GGA_p3 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA ACGGAAAGAGAGGGATTCGA 982–1015 1.000 75.4
ycf3-trnS-GGA_p4 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA CGTGAATTAGGCGAGGGTAC 1000–1033 1.000 75.3
ycf3-trnS-GGA_p5 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA GTGAATTAGGCGAGGGTACG 999–1032 1.000 75.3
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 1407–1541 1.000 85.1
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 1415–1549 1.000 84.5
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 1439–1573 1.000 84.2
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 1447–1581 1.000 83.6
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ATCCAATCAAGTCCGTAGCG 1430–1564 1.000 83.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (17)

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

Species Accession Length (bp) Link
Trollius altaicus NC_084427.1 159986 View on NCBI ↗
Trollius asiaticus NC_084428.1 160002 View on NCBI ↗
Trollius buddae NC_084429.1 159688 View on NCBI ↗
Trollius chinensis NC_031849.1 160191 View on NCBI ↗
Trollius dschungaricus NC_084430.1 159816 View on NCBI ↗
Trollius europaeus PP622705.1 159997 View on NCBI ↗
Trollius farreri NC_050872.1 160611 View on NCBI ↗
Trollius japonicus NC_084431.1 160061 View on NCBI ↗
Trollius ledebouri NC_084432.1 160025 View on NCBI ↗
Trollius lilacinus NC_084433.1 160202 View on NCBI ↗
Trollius macropetalus NC_059918.1 160094 View on NCBI ↗
Trollius micranthus NC_084434.1 159597 View on NCBI ↗
Trollius pumilus NC_084435.1 159598 View on NCBI ↗
Trollius ranunculoides NC_084436.1 159616 View on NCBI ↗
Trollius taihasenzanensis NC_084437.1 160019 View on NCBI ↗
Trollius vaginatus NC_084438.1 159723 View on NCBI ↗
Trollius yunnanensis NC_084439.1 159717 View on NCBI ↗