Markers + reference

Rhodoleia

3 species · Hamamelidaceae · Saxifragales

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Species 3
Genome length 159–159 kb
Candidate markers 276
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 276 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1747 0.0042 0.99 58.2 yes View details
petN-psbM LSC 864 0.0069 1.00 49.1 yes View details
rps4-trnT-UGU LSC 344 0.0097 1.00 51.3 yes View details
ndhC-trnV-UAC LSC 1192 0.0068 0.99 64.8 yes View details
accD LSC 1467 0.0027 1.00 45.7 yes View details
ycf4-cemA LSC 903 0.0037 0.99 50.3 yes View details
petA-psbJ LSC 808 0.0091 1.00 62.7 yes View details
rpl20 LSC 354 0.0038 1.00 30.9 yes View details
ccsA-ndhD SSC 303 0.0221 1.00 61.0 yes View details
ndhD SSC 1503 0.0027 1.00 46.6 yes View details
rps15 SSC 273 0.0024 1.00 28.5 yes View details
ndhH-rps15 SSC 100 0.0539 0.99 73.4 yes View details
trnT-UGU-trnL-UAA LSC 1134 0.0050 0.95 66.1 yes View details
trnE-UUC-trnT-GGU LSC 682 0.0053 0.93 65.8 yes View details
psaA-ycf3 LSC 665 0.0040 1.00 61.5 yes View details
rpl32-trnL-UAG SSC 659 0.0031 0.99 61.5 yes View details
atpF-atpH LSC 392 0.0069 0.99 61.1 yes View details
matK LSC 1512 0.0031 1.00 60.7 yes View details
ndhF-rpl32 SSC 862 0.0031 1.00 60.7 yes View details
trnF-GAA-ndhJ LSC 700 0.0029 1.00 60.6 yes View details
atpH-atpI LSC 1129 0.0006 0.99 59.7 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK_p1 matK TCAACCCTTACTGCATGAACA ACCTGTCTCCGAGGTATCTA 1740 1.000 54.6
matK_p2 matK TCAACCCTTACTGCATGAACA TACCTGTCTCCGAGGTATCT 1741 1.000 54.6
matK_p3 matK TCAACCCTTACTGCATGAACA TTACCTGTCTCCGAGGTATCT 1742 1.000 52.7
matK_p4 matK TCAACCCTTACTGCATGAACA CCTTGTTTTGACTGTATCGCA 1701 1.000 51.0
matK_p5 matK TCAACCCTTACTGCATGAACA ACCTTGTTTTGACTGTATCGC 1702 1.000 51.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1820–1832 1.000 79.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1831–1843 1.000 78.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1841–1853 1.000 76.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 1842–1854 1.000 76.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCCACAGCTGATCATGTCC GAGGTTCGAATCCTTCCGTC 1843–1855 1.000 75.2
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG CGGAGGGAAAAATACGAGGT 572–576 1.000 75.5
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG CGAGGCGGAGGGAAAAATAC 577–581 1.000 75.4
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG GAGGCGGAGGGAAAAATACG 576–580 1.000 75.4
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GCGGAGGGAAAAATACGAGG 573–577 1.000 75.4
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG GGCGGAGGGAAAAATACGAG 574–578 1.000 75.4
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1217–1246 1.000 76.1
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCAACTTTAGCCGCG 1273–1302 1.000 75.5
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT AGGCGAATCTATGGAGGGTC 1189–1218 1.000 75.0
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 1218–1247 1.000 74.9
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC TTTTTGCAACTTTAGCCGCG 1277–1306 1.000 74.8
petN-psbM_p1 petN-psbM ATAGACAATCGGGAGACGGT AATGGAAGTGGAAAAGCGGT 1821–1825 1.000 80.1
petN-psbM_p2 petN-psbM TGTAATTCTCCCGATCCCGA AATGGAAGTGGAAAAGCGGT 1840–1844 1.000 80.0
petN-psbM_p3 petN-psbM AATCGGGAGACGGTAAGGAT AATGGAAGTGGAAAAGCGGT 1815–1819 1.000 80.0
petN-psbM_p4 petN-psbM ATCGGGAGACGGTAAGGATT AATGGAAGTGGAAAAGCGGT 1814–1818 1.000 80.0
petN-psbM_p5 petN-psbM TTCTCCCGATCCCGATAGAC AATGGAAGTGGAAAAGCGGT 1835–1839 1.000 79.9
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 767–823 1.000 83.2
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TACCGCTGAGTTAAAAGGGC 732–788 1.000 82.4
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 729–785 1.000 82.4
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCGATGACTTACGCCTTACC 764–820 1.000 82.0
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TACCGCTGAGTTAAAAGGGC 694–750 1.000 81.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Rhodoleia championii NC_045276.1 159115 View on NCBI ↗
Rhodoleia henryi NC_071196.1 159047 View on NCBI ↗
Rhodoleia parvipetala NC_071828.1 159117 View on NCBI ↗