Markers + reference

Hemsleya

4 species · Cucurbitaceae · Cucurbitales

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Species 4
Genome length 157–158 kb
Candidate markers 272
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnR-UCU-atpA LSC 368 0.0100 1.00 37.4 yes View details
rpoB-trnC-GCA LSC 1195 0.0043 1.00 54.8 yes View details
psbM-trnD-GUC LSC 1074 0.0678 0.95 79.7 yes View details
trnT-GGU-psbD LSC 1517 0.0060 1.00 50.5 yes View details
ycf1 IRb 1191 0.0004 1.00 36.5 no View details
ndhF-rpl32 SSC 637 0.0065 1.00 49.8 yes View details
rpl32-trnL-UAG SSC 1186 0.0060 1.00 40.2 yes View details
ccsA SSC 972 0.0045 1.00 37.9 yes View details
ycf1 SSC 5637 0.0038 1.00 35.2 yes View details
rps16-trnQ-UUG LSC 1738 0.0043 1.00 60.1 yes View details
psaA LSC 2253 0.0007 1.00 57.6 yes View details
rps4 LSC 606 0.0025 1.00 55.5 yes View details
rpl2-trnH-GUG LSC 76 0.0066 1.00 53.5 no View details
trnF-GAA-ndhJ LSC 728 0.0023 1.00 52.9 yes View details
trnR-ACG-trnN-GUU IRb 617 0.0051 1.00 52.7 yes View details
trnN-GUU-trnR-ACG IRa 617 0.0051 1.00 52.7 yes View details
trnE-UUC-trnT-GGU LSC 915 0.0044 1.00 52.4 yes View details
trnT-UGU-trnL-UAA LSC 654 0.0033 1.00 52.4 yes View details
rpl16 LSC 1492 0.0028 1.00 51.5 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1806–1811 1.000 79.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1817–1822 1.000 78.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGGTGGGTGTAAGAATCCAC GAGGTTCGAATCCTTCCGTC 1843–1848 1.000 78.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AACGGTGGGTGTAAGAATCC GAGGTTCGAATCCTTCCGTC 1845–1850 1.000 76.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ACGGTGGGTGTAAGAATCCA GAGGTTCGAATCCTTCCGTC 1844–1849 1.000 75.1
trnR-UCU-atpA_p1 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG TTCCACCAAGACATTCACCG 805–813 1.000 80.3
trnR-UCU-atpA_p2 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG GCTTATCCGGGGGATGTTTT 1380–1388 1.000 80.1
trnR-UCU-atpA_p3 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG GATCCCTCCAAACAAGCACA 1449–1457 1.000 79.9
trnR-UCU-atpA_p4 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG TGATCCCTCCAAACAAGCAC 1450–1458 1.000 79.9
trnR-UCU-atpA_p5 trnR-UCU-atpA CCTAGCCTTCCAAGCTAACG GCTTATCCGGGGGATGTTTT 1383–1391 1.000 79.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CTCTCATTTCCACCCCCAAG GCGTCTTTTGTTGATGAGGC 1302–1308 1.000 79.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CTCTCATTTCCACCCCCAAG CCGGATTTGAACTGGGGAAA 1277–1283 1.000 79.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCTCTCATTTCCACCCCCAA GCGTCTTTTGTTGATGAGGC 1303–1309 1.000 78.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTCTCTCATTTCCACCCCCA GCGTCTTTTGTTGATGAGGC 1304–1310 1.000 78.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCTCTCATTTCCACCCCCAA CCGGATTTGAACTGGGGAAA 1278–1284 1.000 78.3
psbM-trnD-GUC_p1 psbM-trnD-GUC AAAAAGGCGGTAGGAACGAG TTCAATTGGTCAGAGCACCG 1203 1.000 85.9
psbM-trnD-GUC_p2 psbM-trnD-GUC GCGGTAGGAACGAGAATGAA TTCAATTGGTCAGAGCACCG 1197 1.000 85.2
psbM-trnD-GUC_p3 psbM-trnD-GUC ACGAGAATGAACAGTGCAGT TTCAATTGGTCAGAGCACCG 1188 1.000 83.3
psbM-trnD-GUC_p4 psbM-trnD-GUC AAAAAGGCGGTAGGAACGAG GTTCAATTGGTCAGAGCACC 1204 1.000 81.7
psbM-trnD-GUC_p5 psbM-trnD-GUC AAGGCGGTAGGAACGAGAAT TTCAATTGGTCAGAGCACCG 1200 1.000 81.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTAGTACTCTACCCCCAGG GAACCGATGACTTACGCCTT 1048–1053 1.000 80.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTAGTACTCTACCCCCAGG CCATGGCGTTACTCTACCAC 1027–1032 1.000 80.4
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTAGTACTCTACCCCCAGG TGGCGTTACTCTACCACTGA 1024–1029 1.000 80.2
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CGTAGTACTCTACCCCCAGG CCGATGACTTACGCCTTACC 1045–1050 1.000 79.7
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 1013–1018 1.000 78.9
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1667 1.000 78.3
trnT-GGU-psbD_p2 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GACCGGACCAACCTACAAAA 1681 1.000 78.2
trnT-GGU-psbD_p3 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1670 1.000 78.2
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GACCGGACCAACCTACAAAA 1684 1.000 78.0
trnT-GGU-psbD_p5 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG TAGACCGGACCAACCTACAA 1683 1.000 77.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Hemsleya amabilis NC_082823.1 157401 View on NCBI ↗
Hemsleya carnosiflora ON880468.1 157395 View on NCBI ↗
Hemsleya graciliflora NC_082822.1 157781 View on NCBI ↗
Hemsleya zhejiangensis NC_056163.1 157289 View on NCBI ↗