Markers + reference

Mahonia

6 species · Berberidaceae · Ranunculales

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Species 6
Genome length 165–166 kb
Candidate markers 291
Primer pairs 80

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 291 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
accD LSC 1497 0.0117 1.00 51.9 yes View details
rps12-clpP LSC 489 0.0093 1.00 52.2 yes View details
psbB IRb 1527 0.0000 1.00 26.4 no View details
trnI-CAU-ycf2 IRb 330 0.0163 0.95 67.8 yes View details
ycf1 IRb 1335 0.0065 1.00 50.1 yes View details
ccsA SSC 966 0.0007 1.00 32.4 yes View details
ccsA-ndhD SSC 236 0.0412 1.00 65.5 yes View details
ycf1 SSC 5562 0.0033 1.00 43.4 no View details
ycf15-trnI-CAU IRa 6528 0.0007 1.00 54.5 yes View details
psbB IRa 1527 0.0000 1.00 26.4 yes View details
psbB-trnH-GUG IRa 77 0.0563 0.94 91.7 no View details
trnT-UGU-trnL-UAA LSC 761 0.0038 1.00 66.3 yes View details
trnK-UUU-rps16 LSC 591 0.0058 0.99 65.7 yes View details
ndhC-trnV-UAC LSC 1576 0.0029 0.98 63.7 yes View details
petN-psbM LSC 651 0.0031 1.00 61.6 yes View details
rpoB-trnC-GCA LSC 1202 0.0029 1.00 61.5 yes View details
ycf1-ndhF SSC 107 0.0299 1.00 57.4 yes View details
ndhG-ndhI SSC 472 0.0066 0.99 56.5 yes View details
trnS-GCU-trnR-UCU LSC 1711 0.0007 1.00 56.0 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCTACCAACGGTATGGACGA AAAAAGGCGCTCAACCTACA 746–758 1.000 81.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 681–693 1.000 81.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 680–692 1.000 81.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC AAAAAGGCGCTCAACCTACA 695–707 1.000 80.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 690–702 1.000 80.3
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA GATGGGAAAATTTGCGTCCA 1807–1835 1.000 73.0
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU ACGGAAAGAGAGGGATTCGA GATGGGAAAATTTGCGTCCA 1856–1884 1.000 72.0
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA GATGGGAAAATTTGCGTCCAA 1807–1835 1.000 70.7
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA AGATGGGAAAATTTGCGTCC 1808–1836 1.000 70.6
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU GCTTTAGTCCACTCAGCCAT GATGGGAAAATTTGCGTCCA 1793–1821 1.000 70.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA CCGGATTTGAACTGGGGAAA 1357–1367 1.000 79.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA TGGGGAAAAAGGGATTTGCA 1345–1355 1.000 79.7
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA TTATTGATCAGGCGACACCC 1375–1385 1.000 78.0
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AAAGTTCTTCCGTCAAGCCC CCGGATTTGAACTGGGGAAA 1367–1377 1.000 77.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AAAGTTCTTCCGTCAAGCCC TGGGGAAAAAGGGATTTGCA 1355–1365 1.000 76.8
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCATTGTTCATTCT 804–806 1.000 55.7
petN-psbM_p2 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCATTGTTCATTCT 810–812 1.000 54.2
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCATTGTTCATTCT 750–752 1.000 53.0
petN-psbM_p4 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCATTGTTCATTC 804–806 1.000 51.1
petN-psbM_p5 petN-psbM TTGCTTGGGCTGCTTTAATG TGCTACTGCATTGTTCATTCT 802–804 1.000 49.8
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 795–820 1.000 82.6
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 803–828 1.000 82.0
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 827–852 1.000 81.6
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 835–860 1.000 81.0
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ATCCAATCAAGTCCGTAGCG 818–843 1.000 80.7
ndhC-trnV-UAC_p1 ndhC-trnV-UAC CGGTCCTTCACTAATTGGGG AGAAGGTCTACGGTTCGAGT 1685–1723 1.000 80.9
ndhC-trnV-UAC_p2 ndhC-trnV-UAC CCGGTCCTTCACTAATTGGG AGAAGGTCTACGGTTCGAGT 1686–1724 1.000 80.8
ndhC-trnV-UAC_p3 ndhC-trnV-UAC CCTTCACTAATTGGGGCCAA AGAAGGTCTACGGTTCGAGT 1681–1719 1.000 79.3
ndhC-trnV-UAC_p4 ndhC-trnV-UAC GGTCCTTCACTAATTGGGGC AGAAGGTCTACGGTTCGAGT 1684–1722 1.000 79.3
ndhC-trnV-UAC_p5 ndhC-trnV-UAC GTCCTTCACTAATTGGGGCC AGAAGGTCTACGGTTCGAGT 1683–1721 1.000 79.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Mahonia bodinieri NC_066184.1 165697 View on NCBI ↗
Mahonia breviracema NC_066185.1 165555 View on NCBI ↗
Mahonia cardiophylla NC_066186.1 165559 View on NCBI ↗
Mahonia hancockiana NC_066190.1 165495 View on NCBI ↗
Mahonia nanlingensis PP504926.1 165726 View on NCBI ↗
Mahonia shenii NC_066196.1 165928 View on NCBI ↗