Markers + reference

Rubia

7 species · Rubiaceae · Gentianales

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Species 7
Genome length 154–155 kb
Candidate markers 260
Primer pairs 100

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 8 remaining regions by MarkerSeek score (out of 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1430 0.0207 1.00 64.3 yes View details
trnS-GCU-trnS-CGA LSC 918 0.0151 0.98 62.6 yes View details
psbM-trnD-GUC LSC 706 0.0140 1.00 55.8 yes View details
trnT-GGU-psbD LSC 1353 0.0083 0.99 58.2 yes View details
ycf3 LSC 2238 0.0051 1.00 49.5 yes View details
trnT-UGU-trnL-UAA LSC 875 0.0124 1.00 61.0 yes View details
trnP-UGG-psaJ LSC 376 0.0119 1.00 38.5 yes View details
psaJ-rps18 LSC 842 0.0177 0.98 57.5 yes View details
ndhF-rpl32 SSC 748 0.0107 1.00 54.1 yes View details
rpl32-trnL-UAG SSC 663 0.0147 0.98 60.6 yes View details
ndhA SSC 2274 0.0061 0.99 44.4 yes View details
rpl36-rps8 LSC 599 0.0132 0.99 66.6 yes View details
trnK-UUU-rps16 LSC 636 0.0114 1.00 59.9 yes View details
psbH-petB LSC 479 0.0034 1.00 57.9 yes View details
trnH-GUG-psbA LSC 224 0.0254 0.99 57.4 yes View details
rpoB-trnC-GCA LSC 1071 0.0078 1.00 55.2 yes View details
trnE-UUC-trnT-GGU LSC 814 0.0053 1.00 52.9 yes View details
trnG-GCC-trnM-CAU LSC 192 0.0155 1.00 52.3 yes View details
atpA LSC 1518 0.0026 1.00 52.1 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 100 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 AGCTGCTATAGATGCTCCATC 277–287 1.000 70.2
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCTAGCTGCTATAGATGCTCCA 280–290 1.000 68.9
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG AGCTGCTATAGATGCTCCAT 277–287 1.000 68.1
trnH-GUG-psbA_p4 trnH-GUG-psbA GCCTTGATCCACTTGGCTAC AGCTGCTATAGATGCTCCATC 282–292 1.000 66.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCTGCTATAGATGCTCCATC 276–286 1.000 65.9
trnK-UUU_p1 trnK-UUU GTGACCTCGATCGATTCACA ACGGTTTAATTCCCTCGTCTG 2705–2732 0.857 63.3
trnK-UUU_p2 trnK-UUU GTGACCTCGATCGATTCACA CGGTTTAATTCCCTCGTCTGA 2704–2731 0.857 61.7
trnK-UUU_p3 trnK-UUU CAGTGACCTCGATCGATTCA ACGGTTTAATTCCCTCGTCTG 2707–2734 0.857 61.0
trnK-UUU_p4 trnK-UUU ACAGTGACCTCGATCGATTC ACGGTTTAATTCCCTCGTCTG 2708–2735 0.857 61.0
trnK-UUU_p5 trnK-UUU AGTGACCTCGATCGATTCAC ACGGTTTAATTCCCTCGTCTG 2706–2733 0.857 61.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TGCTCAACTTACAGGAACCG 744–786 1.000 79.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GCTCAACTTACAGGAACCGT 743–785 1.000 79.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA TGCTCAACTTACAGGAACCG 742–784 1.000 77.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GCTCAACTTACAGGAACCGT 741–783 1.000 77.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 TAGTCGCACTTAAAAGCCGA TGCTCAACTTACAGGAACCG 745–787 1.000 77.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 842–1539 1.000 86.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 846–1543 1.000 82.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 872–1569 1.000 82.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 834–1531 1.000 81.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 841–1538 1.000 81.1
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA AAACCGAAAGCAAAGACCCT 698–1074 1.000 86.6
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA AACCGAAAGCAAAGACCCTT 697–1073 1.000 86.6
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA ACCGAAAGCAAAGACCCTTT 696–1072 1.000 86.6
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA AATCCGACGCTTTAGTCCAC AACCGAAAGCAAAGACCCTT 696–1072 1.000 86.6
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA AATCCGACGCTTTAGTCCAC ACCGAAAGCAAAGACCCTTT 695–1071 1.000 86.6
atpA_p1 atpA AGCCTTCCAAGCTAACGATG TCAAGTTCGACAACGGGTTT 2173–2226 1.000 82.4
atpA_p2 atpA AGTTTCGGGTTCGGTTTTGA TCAAGTTCGACAACGGGTTT 2238–2291 1.000 82.2
atpA_p3 atpA CCTAGCCTTCCAAGCTAACG TCAAGTTCGACAACGGGTTT 2176–2229 1.000 82.2
atpA_p4 atpA AGCCTTCCAAGCTAACGATG GGGAAGGGGCTATTGAACAG 2376–2428 0.857 75.8
atpA_p5 atpA AGTTTCGGGTTCGGTTTTGA GGGAAGGGGCTATTGAACAG 2441–2493 0.857 75.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Rubia alata NC_083086.1 154973 View on NCBI ↗
Rubia cordifolia NC_047470.1 153555 View on NCBI ↗
Rubia ovatifolia NC_083087.1 154866 View on NCBI ↗
Rubia podantha NC_061256.1 154866 View on NCBI ↗
Rubia tibetica PQ249606.1 154901 View on NCBI ↗
Rubia tinctorum PP836148.1 154312 View on NCBI ↗
Rubia yunnanensis NC_061257.1 155108 View on NCBI ↗