Markers + reference

Stewartia

21 species · Theaceae · Ericales

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Species 21
Genome length 158–159 kb
Candidate markers 273
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 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 803 0.0075 0.99 60.9 yes View details
trnT-UGU-trnL-UAA LSC 993 0.0073 1.00 64.6 yes View details
accD-psaI LSC 729 0.0114 1.00 64.3 yes View details
petA-psbJ LSC 1041 0.0067 1.00 59.5 yes View details
rpoA LSC 1014 0.0031 1.00 37.9 yes View details
trnN-GUU-ndhF IRb 1706 0.0034 1.00 59.0 yes View details
ndhF SSC 2253 0.0062 1.00 45.7 yes View details
ndhF-rpl32 SSC 858 0.0095 0.97 54.6 yes View details
rps15-ycf1 SSC 381 0.0129 1.00 41.7 yes View details
ycf1 SSC 5655 0.0060 1.00 46.4 yes View details
trnT-GGU-psbD LSC 1516 0.0065 0.99 62.9 yes View details
rps16-trnQ-UUG LSC 1765 0.0054 0.99 57.5 yes View details
lhbA-trnG-UCC LSC 284 0.0074 0.98 57.2 yes View details
psbM-trnD-GUC LSC 1133 0.0032 1.00 55.8 yes View details
psaA-ycf3 LSC 736 0.0029 1.00 55.3 yes View details
rpl16 LSC 1452 0.0050 1.00 54.9 yes View details
atpH-atpI LSC 1145 0.0032 1.00 54.3 yes View details
trnS-GCU-trnG LSC 680 0.0046 1.00 53.8 yes View details
trnF-GAA-ndhJ LSC 708 0.0052 1.00 53.3 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 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 CGAATCCCTTGCTTCATCCA GGTGCTCAACCTACAGAAACT 972–982 1.000 74.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC GGTGCTCAACCTACAGAAACT 973–983 1.000 74.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 ATGGACGAATCCCTTGCTTC GGTGCTCAACCTACAGAAACT 977–987 1.000 74.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT GGTGCTCAACCTACAGAAACT 975–985 1.000 74.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGAAACT 923–933 1.000 73.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1670–1874 1.000 84.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1653–1857 1.000 84.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1671–1875 1.000 83.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1668–1872 1.000 82.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1667–1871 1.000 82.3
trnS-GCU-trnG_p1 trnS-GCU-trnG ATTAGCAATCCGCCGCTTTA AACCGAAAGACCCCTTAACT 791–817 1.000 68.7
trnS-GCU-trnG_p2 trnS-GCU-trnG CTTTAGTCCACTCAGCCACC AACCGAAAGACCCCTTAACT 776–802 1.000 68.3
trnS-GCU-trnG_p3 trnS-GCU-trnG ACGGAAAGAGAGGGATTCGA AACCGAAAGACCCCTTAACT 840–866 1.000 67.7
trnS-GCU-trnG_p4 trnS-GCU-trnG TTTAGTCCACTCAGCCACCT AACCGAAAGACCCCTTAACT 775–801 1.000 66.9
trnS-GCU-trnG_p5 trnS-GCU-trnG ATTAGCAATCCGCCGCTTTA AAACCGAAAGACCCCTTAACT 792–818 1.000 66.8
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1231–1235 1.000 77.4
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCAACTTTAGCCGCG 1287–1291 1.000 76.7
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 1232–1236 1.000 76.2
atpH-atpI_p4 atpH-atpI GCAGTACCTTGACCAACTCC TTTTTGCAACTTTAGCCGCG 1291–1295 1.000 76.1
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTTGCAACTTTAGCCGCG 1246–1250 1.000 75.9
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1243–1262 1.000 60.6
psbM-trnD-GUC_p2 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA TTCAATTGGTCAGAGCACCG 1250–1269 1.000 57.4
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC GTTCAATTGGTCAGAGCACC 1244–1263 1.000 56.4
psbM-trnD-GUC_p4 psbM-trnD-GUC GGAACTAGAATGAACAGTGCAG TTCAATTGGTCAGAGCACCG 1249–1268 1.000 54.9
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TCAATTGGTCAGAGCACCG 1242–1261 1.000 54.6
trnT-GGU-psbD_p1 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GGACCAGCCTACAAAAACGA 1636–1663 1.000 82.1
trnT-GGU-psbD_p2 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA GGACCAGCCTACAAAAACGA 1673–1700 0.952 80.8
trnT-GGU-psbD_p3 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA ACAAAAACGAAACGGTCCCT 1663–1690 0.952 79.8
trnT-GGU-psbD_p4 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA CAAAAACGAAACGGTCCCTC 1662–1689 0.952 78.6
trnT-GGU-psbD_p5 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA AGAGCAATAAACCGGACCAG 1686–1713 0.952 78.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (21)

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

Species Accession Length (bp) Link
Stewartia calcicola NC_035696.1 158425 View on NCBI ↗
Stewartia cordifolia NC_035649.1 158450 View on NCBI ↗
Stewartia crassifolia NC_035647.1 158410 View on NCBI ↗
Stewartia malacodendron NC_035691.1 158376 View on NCBI ↗
Stewartia micrantha NC_041471.1 158467 View on NCBI ↗
Stewartia monadelpha NC_041468.1 158447 View on NCBI ↗
Stewartia obovata NC_041472.1 158569 View on NCBI ↗
Stewartia ovata NC_035695.1 158416 View on NCBI ↗
Stewartia pseudocamellia NC_035697.1 158409 View on NCBI ↗
Stewartia pseudocamellia var. koreana MH782176.1 158191 View on NCBI ↗
Stewartia pteropetiolata NC_035690.1 158520 View on NCBI ↗
Stewartia rostrata NC_035698.1 158077 View on NCBI ↗
Stewartia rubiginosa NC_035650.1 158433 View on NCBI ↗
Stewartia serrata NC_041467.1 158356 View on NCBI ↗
Stewartia sichuanensis NC_070087.1 158903 View on NCBI ↗
Stewartia sinensis NC_035640.1 158177 View on NCBI ↗
Stewartia sinensis var. acutisepala MH782177.1 158481 View on NCBI ↗
Stewartia sinensis var. shensiensis MH753078.1 158395 View on NCBI ↗
Stewartia sinensis var. sinensis OQ948159.1 158406 View on NCBI ↗
Stewartia sinii NC_041470.1 158478 View on NCBI ↗
Stewartia villosa NC_041469.1 158536 View on NCBI ↗