Markers + reference

Castanopsis

11 species · Fagaceae · Fagales

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Species 11
Genome length 160–161 kb
Candidate markers 263
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 11 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 835 0.0104 1.00 61.9 yes View details
psbK-psbI LSC 437 0.0164 1.00 62.5 yes View details
rpoB-trnF-GAA LSC 1224 0.0071 1.00 66.7 yes View details
psbM-trnD-GUC LSC 1247 0.0040 1.00 60.2 yes View details
ycf3 LSC 1995 0.0022 1.00 45.6 yes View details
rbcL-accD LSC 575 0.0210 1.00 49.0 yes View details
ndhF SSC 2268 0.0033 1.00 39.6 yes View details
ccsA-ndhD SSC 300 0.0078 1.00 35.9 yes View details
ndhG SSC 546 0.0025 1.00 30.7 yes View details
ndhI-ndhA SSC 1577 0.0034 1.00 63.1 yes View details
rpl2-trnH-GUG IRa 77 0.0362 0.92 65.8 no View details
psbE-petL LSC 1247 0.0037 1.00 61.5 yes View details
trnS-GCU-trnG-GCC LSC 942 0.0034 1.00 61.1 yes View details
ndhI SSC 603 0.0017 1.00 59.5 yes View details
rpoC1 LSC 2909 0.0021 1.00 58.2 yes View details
rpl16-rps3 LSC 1252 0.0032 1.00 58.0 yes View details
ycf1 SSC 5682 0.0019 1.00 57.8 yes View details
ndhE-ndhG SSC 257 0.0126 0.99 57.7 yes View details
trnE-UUC-trnT-GGU LSC 1002 0.0013 1.00 57.4 yes View details
psaJ-rpl33 LSC 463 0.0051 1.00 56.7 yes View details
ycf1 SSC 1158 0.0008 1.00 46.7 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TATTTCCTTGAAAGGGGCGC 963–979 1.000 80.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TATTTCCTTGAAAGGGGCGC 962–978 1.000 80.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CGAAGAAGGCGGGAGTTTTT 913–929 1.000 78.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TATTTCGAAGAAGGCGGGAG 919–935 0.909 76.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TATTTCGAAGAAGGCGGGAG 918–934 0.909 76.5
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG CTTCACTCTTCACGTCCAGG 537–557 1.000 85.1
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCACTCTTCACGTCCAGGAT 535–555 1.000 85.1
psbK-psbI_p3 psbK-psbI CTTTTGTTTGGCAAGCTGCT CTTCACTCTTCACGTCCAGG 542–562 1.000 85.0
psbK-psbI_p4 psbK-psbI CTTTTGTTTGGCAAGCTGCT TCACTCTTCACGTCCAGGAT 540–560 1.000 85.0
psbK-psbI_p5 psbK-psbI CTTTTGTTTGGCAAGCTGCT TTCACTCTTCACGTCCAGGA 541–561 1.000 83.2
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CGAAGGACCCCTTAACCATT 1045–1096 1.000 76.0
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC CGAAGGACCCCTTAACCATT 1044–1095 1.000 76.0
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC TAGTCCACTCAGCCATCTCC CGAAGGACCCCTTAACCATT 1032–1083 1.000 74.4
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CGAAGGACCCCTTAACCATTT 1045–1096 1.000 73.8
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC CGAAGGACCCCTTAACCATTT 1044–1095 1.000 73.8
rpoC1_p1 rpoC1 ACCAGAGAGACACTAATTCACA CCAGATGAATAGGAAGGAAGCT 2998–3000 0.273 11.4
rpoC1_p2 rpoC1 ACCAGAGAGACACTAATTCACA TCCAGATGAATAGGAAGGAAGC 2999–3000 0.182 7.6
rpoC1_p3 rpoC1 AACCAGAGAGACACTAATTCACA CCAGATGAATAGGAAGGAAGCT 2999–3000 0.182 7.6
rpoC1_p4 rpoC1 AACCAGAGAGACACTAATTCACA TCCAGATGAATAGGAAGGAAGC 3000 0.091 3.6
rpoC1_p5 rpoC1 ACCAGAGAGACACTAATTCACA TTCCAGATGAATAGGAAGGAAGC 3000 0.091 3.6
rpoB-trnF-GAA_p1 rpoB-trnF-GAA CCTCATTTCTACCCCCAAGC TTAGGCGACACCCAGATTTG 1240–1466 1.000 84.7
rpoB-trnF-GAA_p2 rpoB-trnF-GAA CCTCATTTCTACCCCCAAGC TTGTTGATTAGGCGACACCC 1247–1473 1.000 84.1
rpoB-trnF-GAA_p3 rpoB-trnF-GAA CCTCATTTCTACCCCCAAGC AAAAGGATTTGCAGTCCCCC 1211–1437 1.000 82.7
rpoB-trnF-GAA_p4 rpoB-trnF-GAA TCCCTCATTTCTACCCCCAA TTAGGCGACACCCAGATTTG 1242–1468 1.000 82.2
rpoB-trnF-GAA_p5 rpoB-trnF-GAA TTCCCTCATTTCTACCCCCA TTAGGCGACACCCAGATTTG 1243–1469 1.000 82.2
psbM-trnD-GUC_p1 psbM-trnD-GUC CGGAACTAGAATGAACAGTGC TTCAATTGGTCAGAGCACCG 1355–1370 1.000 62.0
psbM-trnD-GUC_p2 psbM-trnD-GUC AGCAGTCGGAACTAGAATGA TTCAATTGGTCAGAGCACCG 1361–1376 1.000 61.9
psbM-trnD-GUC_p3 psbM-trnD-GUC AGCAGTCGGAACTAGAATGAAC TTCAATTGGTCAGAGCACCG 1361–1376 1.000 60.8
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1348–1363 1.000 60.2
psbM-trnD-GUC_p5 psbM-trnD-GUC AGCAGTCGGAACTAGAATGAA TTCAATTGGTCAGAGCACCG 1361–1376 1.000 60.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Castanopsis concinna NC_033409.1 160606 View on NCBI ↗
Castanopsis echinocarpa NC_023801.1 160647 View on NCBI ↗
Castanopsis faberi OQ024219.1 160518 View on NCBI ↗
Castanopsis fordii NC_065323.1 160853 View on NCBI ↗
Castanopsis hainanensis NC_037389.1 160631 View on NCBI ↗
Castanopsis hystrix NC_061039.1 160624 View on NCBI ↗
Castanopsis mekongensis NC_053865.1 160669 View on NCBI ↗
Castanopsis orthacantha NC_085533.1 160588 View on NCBI ↗
Castanopsis sclerophylla NC_044680.1 160497 View on NCBI ↗
Castanopsis tibetana NC_065324.1 160468 View on NCBI ↗
Castanopsis wenchangensis NC_084325.1 160635 View on NCBI ↗