Markers + reference

Dobinea

2 species · Anacardiaceae · Sapindales

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Species 2
Genome length 160–161 kb
Candidate markers 270
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 8 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 570 0.0437 0.96 86.6 yes View details
psbA-trnK-UUU LSC 254 0.0315 1.00 68.1 yes View details
rps16-trnQ-UUG LSC 1301 0.0108 1.00 64.9 yes View details
trnQ-UUG-psbK LSC 360 0.0111 1.00 52.3 yes View details
psbM-trnD-GUC LSC 1069 0.0131 1.00 63.3 yes View details
trnM-CAU-psbD LSC 1565 0.0092 0.97 58.9 yes View details
trnT-UGU-trnL-UAA LSC 914 0.0132 1.00 56.5 yes View details
petA-psbJ LSC 1101 0.0109 1.00 62.2 yes View details
ndhF-rpl32 SSC 1024 0.0128 0.99 66.9 yes View details
rpl32-trnL-UAG SSC 1071 0.0132 0.99 66.4 yes View details
trnG-GCC-trnfM-CAU LSC 161 0.0187 0.99 63.9 yes View details
rps7-rps12 IRb 53 0.0189 1.00 63.3 yes View details
ndhI-ndhA SSC 81 0.0247 1.00 63.3 yes View details
rps12-rps7 IRa 53 0.0189 1.00 63.3 yes View details
psbE-petL LSC 1487 0.0074 1.00 63.2 yes View details
trnE-UUC-trnM-CAU LSC 679 0.0074 1.00 63.1 yes View details
rbcL-accD LSC 629 0.0064 1.00 62.6 yes View details
ndhC-trnV-UAC LSC 625 0.0096 1.00 62.3 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 689–708 1.000 81.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 703–722 1.000 81.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 702–721 1.000 81.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 704–723 1.000 81.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 690–709 1.000 80.9
psbA-trnK-UUU_p1 psbA-trnK-UUU TACAGAAGCGACCCCATAGG AATGAAAAATGCAGGCACGG 421 1.000 76.1
psbA-trnK-UUU_p2 psbA-trnK-UUU TACAGAAGCGACCCCATAGG CGGCTTGGGGAGAGATTTTT 404 1.000 75.6
psbA-trnK-UUU_p3 psbA-trnK-UUU ATCCAGTTACAGAAGCGACC AATGAAAAATGCAGGCACGG 428 1.000 75.4
psbA-trnK-UUU_p4 psbA-trnK-UUU AGTTACAGAAGCGACCCCAT AATGAAAAATGCAGGCACGG 424 1.000 75.1
psbA-trnK-UUU_p5 psbA-trnK-UUU ATCCAGTTACAGAAGCGACC CGGCTTGGGGAGAGATTTTT 411 1.000 74.9
trnK-UUU_p1 trnK-UUU TCTCCGTGTCAACCAATAGT CCATCCCATAGGTTTGGCTC 2993 0.500 45.4
trnK-UUU_p2 trnK-UUU TCTCCGTGTCAACCAATAGT CTCCATCCCATAGGTTTGGC 2995 0.500 45.4
trnK-UUU_p3 trnK-UUU TCTCCGTGTCAACCAATAGT TGGCTCATGGGTTTGGTTTT 2979 0.500 43.9
trnK-UUU_p4 trnK-UUU TCTCCGTGTCAACCAATAGT TTGGCTCATGGGTTTGGTTT 2980 0.500 43.9
trnK-UUU_p5 trnK-UUU TCTCCGTGTCAACCAATAGT TTTGGCTCATGGGTTTGGTT 2981 0.500 43.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1431–1513 1.000 79.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAAATTGAAATGGGGCGTGG 1442–1524 1.000 79.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1374–1455 1.000 79.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GCTATCGGAGGTTCGAATCC 1381 0.500 58.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GCTATCGGAGGTTCGAATCC 1392 0.500 57.8
trnQ-UUG-psbK_p1 trnQ-UUG-psbK AGTACACTCTGGGACGGAAG CGGGCAATTTGGCGAATAAA 521–522 1.000 74.7
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GAGTACACTCTGGGACGGAA CGGGCAATTTGGCGAATAAA 522–523 1.000 74.7
trnQ-UUG-psbK_p3 trnQ-UUG-psbK GGATTCGAACCTCCGATAGC CGGGCAATTTGGCGAATAAA 502 0.500 57.2
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GATTCGAACCTCCGATAGCG CGGGCAATTTGGCGAATAAA 501 0.500 55.2
trnQ-UUG-psbK_p5 trnQ-UUG-psbK GGATTCGAACCTCCGATAGC TCGGGCAATTTGGCGAATAA 503 0.500 55.2
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TGTCCCGGGATTGTAGTTCA 1196–1204 1.000 60.4
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1180–1188 1.000 59.4
psbM-trnD-GUC_p3 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA TGTCCCGGGATTGTAGTTCA 1203–1211 1.000 57.2
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC GTCCCGGGATTGTAGTTCAA 1195–1203 1.000 57.0
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTGTCCCGGGATTGTAGTTC 1197–1205 1.000 57.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Dobinea delavayi NC_069618.1 160156 View on NCBI ↗
Dobinea vulgaris NC_069619.1 160680 View on NCBI ↗