Markers + reference

Daphne

19 species · Thymelaeaceae · Malvales

Back to catalogue

Species 19
Genome length 171–173 kb
Candidate markers 273
Primer pairs 95

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 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 331 0.0387 1.00 75.0 yes View details
rps16-trnQ-UUG LSC 1278 0.0204 0.94 67.5 yes View details
trnS-GCU-trnG-UCC LSC 757 0.0233 1.00 70.2 yes View details
atpH-atpI LSC 852 0.0201 1.00 72.0 yes View details
psbM-trnD-GUC LSC 749 0.0201 1.00 74.1 yes View details
trnT-UGU-trnL-UAA LSC 948 0.0215 0.95 71.8 yes View details
accD-psaI LSC 732 0.0278 0.99 69.5 yes View details
rpl16 LSC 1484 0.0154 0.98 66.7 yes View details
trnL-UAG-rpl32 SSC 3055 0.0223 1.00 70.1 yes View details
rps19-rpl2 IRb 58 0.0689 0.97 76.2 yes View details
petN-psbM LSC 907 0.0176 1.00 72.8 yes View details
trnG-GCC-trnfM-CAU LSC 154 0.0433 1.00 72.8 yes View details
psbZ-trnG-GCC LSC 533 0.0174 1.00 71.5 yes View details
trnE-UUC-trnT-GGU LSC 670 0.0184 1.00 71.0 yes View details
rpoB-trnC-GCA LSC 1158 0.0136 1.00 69.5 yes View details
psbE-petL LSC 1410 0.0154 1.00 69.5 yes View details
trnK-UUU-rps16 LSC 686 0.0144 1.00 67.6 yes View details
ycf3-trnS-GGA LSC 586 0.0136 1.00 67.6 yes View details
trnT-GGU-psbD LSC 1271 0.0139 1.00 66.7 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 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 CTGCCTTAATCCACTTGGCT TCCCTCTAGATCTAGCTGCT 393–433 1.000 77.6
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TCCCTCTAGATCTAGCTGCT 394–434 1.000 77.4
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGATCTAGCTGCT 394–434 1.000 75.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TTCCCTCTAGATCTAGCTGCT 395–435 1.000 75.6
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTTGGCTACATCCG TCCCTCTAGATCTAGCTGCT 386–426 0.947 73.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTTAAAGAAGGCGGGGGTTT 692–777 0.947 82.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTTTAAAGAAGGCGGGGGTT 693–778 0.947 82.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTAAAGAAGGCGGGGGTTT 691–776 0.947 82.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTTAAAGAAGGCGGGGGTT 692–777 0.947 82.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CGGGGGTTTACGGAACTTAA 680–765 0.947 81.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTTGGTCCCGCTATTCGAAG 1267–1397 1.000 90.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CCACATCGCTTCAAACGAAG TTTGGTCCCGCTATTCGAAG 1247–1377 1.000 89.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTTTTGGTCCCGCTATTCGA 1269–1399 1.000 88.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ACCACATCGCTTCAAACGAA TTTGGTCCCGCTATTCGAAG 1248–1378 1.000 88.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TACCACATCGCTTCAAACGA TTTGGTCCCGCTATTCGAAG 1249–1379 1.000 88.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 499–885 1.000 63.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 498–884 1.000 63.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CGCACAACGGATTAGCAATC ACGAATCACACTTTTACCACT 514–900 1.000 63.0
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 502–888 1.000 62.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 501–887 1.000 62.6
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATGGAGGGTCATCATTGA 897–1275 1.000 50.6
atpH-atpI_p2 atpH-atpI AGCGGCAGAAATCAATGGAT ATGGAGGGTCATCATTGA 889–1267 1.000 50.6
atpH-atpI_p3 atpH-atpI AAGCGGCAGAAATCAATGGA ATGGAGGGTCATCATTGA 890–1268 1.000 50.6
atpH-atpI_p4 atpH-atpI GCAAGTCCTACAGCTAACCC ATGGAGGGTCATCATTGA 924–1302 1.000 50.4
atpH-atpI_p5 atpH-atpI CAGGCCCAATAGAAGCAAGT ATGGAGGGTCATCATTGA 938–1316 1.000 50.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCATTTTCATCCCCGAGCAT CTGGGGTAAAGGGATTTGCA 1193–1242 1.000 85.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCATTTTCATCCCCGAGCAT TGGGGTAAAGGGATTTGCAG 1192–1241 1.000 85.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCATTTTCATCCCCGAGCAT ACTGGGGTAAAGGGATTTGC 1194–1243 1.000 85.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCATTTTCATCCCCGAGCAT GGGGTAAAGGGATTTGCAGT 1191–1240 1.000 85.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ATTCCCCCATTTTCATCCCC TGGGGTAAAGGGATTTGCAG 1198–1247 1.000 83.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (19)

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

Species Accession Length (bp) Link
Daphne acutiloba NC_056317.1 171211 View on NCBI ↗
Daphne aurantiaca NC_062858.1 173057 View on NCBI ↗
Daphne blagayana BK071447.1 171748 View on NCBI ↗
Daphne cneorum BK071448.1 171088 View on NCBI ↗
Daphne depauperata NC_057149.1 170916 View on NCBI ↗
Daphne feddei NC_056320.1 171084 View on NCBI ↗
Daphne giraldii NC_044085.1 171643 View on NCBI ↗
Daphne kamtschatica PV752464.1 171100 View on NCBI ↗
Daphne kiusiana NC_035896.1 171491 View on NCBI ↗
Daphne kiusiana var. atrocaulis NC_060495.1 172163 View on NCBI ↗
Daphne laureola MN201546.1 171613 View on NCBI ↗
Daphne mezereum BK070978.1 170915 View on NCBI ↗
Daphne mucronata PQ858248.1 171190 View on NCBI ↗
Daphne odora NC_060829.1 171156 View on NCBI ↗
Daphne pseudomezereum var. koreana ON244034.1 171152 View on NCBI ↗
Daphne pseudomezereum var. pseudomezereum PV752465.1 171019 View on NCBI ↗
Daphne reichsteinii PP335054.1 172081 View on NCBI ↗
Daphne retusa NC_057148.1 170553 View on NCBI ↗
Daphne striata PP335055.1 171414 View on NCBI ↗