Markers + reference

Dendrocnide

4 species · Urticaceae · Rosales

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Species 4
Genome length 153–153 kb
Candidate markers 266
Primer pairs 110

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 720 0.0095 1.00 50.1 yes View details
rps16 LSC 979 0.0100 1.00 42.4 yes View details
psbK-psbI LSC 444 0.0131 1.00 44.6 yes View details
trnS-GCU-trnG-UCC LSC 652 0.0095 1.00 50.5 yes View details
rpoB-trnC-GCA LSC 1150 0.0059 0.99 47.8 yes View details
trnG-GCC-trnfM-CAU LSC 181 0.0239 1.00 54.9 yes View details
trnT-trnL-UAA LSC 812 0.0115 1.00 51.4 yes View details
petA-psbJ LSC 835 0.0084 1.00 53.8 yes View details
rps18-rpl20 LSC 271 0.0141 1.00 40.8 yes View details
ndhF SSC 2259 0.0068 1.00 37.7 yes View details
ndhE-ndhG SSC 232 0.0216 1.00 42.8 yes View details
ndhA SSC 2293 0.0050 1.00 40.2 yes View details
ycf1 SSC 5613 0.0053 1.00 44.3 yes View details
ycf3-trnS-GGA LSC 887 0.0105 1.00 65.7 yes View details
psbE-petL LSC 1096 0.0056 1.00 63.5 yes View details
atpB-rbcL LSC 781 0.0036 1.00 61.8 yes View details
rpl2-trnH-GUG IRa 167 0.0000 1.00 58.4 no View details
psaA-ycf3 LSC 730 0.0048 1.00 58.0 yes View details
ndhI-ndhA SSC 82 0.0183 1.00 55.9 yes View details
psbZ-trnG-GCC LSC 476 0.0091 1.00 55.7 yes View details
rps4-trnT LSC 518 0.0058 1.00 54.9 yes View details
trnG-UCC-trnR-UCU LSC 247 0.0189 0.97 54.0 yes View details
trnH-GUG-psbA LSC 213 0.0125 1.00 53.9 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 110 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 TGGGCTGATATCATCAACCG 346–353 1.000 76.6
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGGCTGATATCATCAACCGT 345–352 1.000 76.6
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TGGGCTGATATCATCAACCG 360–367 1.000 76.5
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TGGGCTGATATCATCAACCG 359–366 1.000 76.5
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TGGGCTGATATCATCAACCG 361–368 1.000 76.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC GCTCAGCCTACAGGAACTTT 878–895 1.000 78.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT GCTCAGCCTACAGGAACTTT 877–894 1.000 78.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCTCAGCCTACAGGAACTTT 794–811 1.000 77.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAGCCTACAGGAACTTT 793–810 1.000 77.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 CAGTCGCGGTCTTACAAACT GCTCAGCCTACAGGAACTTT 879–896 1.000 77.0
rps16_p1 rps16 TTTTCGGCGCAATCAAAACA CGTAGGTTCGAATCCTTCCG 1846–1877 1.000 79.5
rps16_p2 rps16 GGTTGGTGATTAGGGTGGTG CGTAGGTTCGAATCCTTCCG 1225 0.500 57.4
rps16_p3 rps16 GTTGGTGATTAGGGTGGTGG CGTAGGTTCGAATCCTTCCG 1224 0.500 57.4
rps16_p4 rps16 GGTTGGTGATTAGGGTGGTG GTTTTGGTCCCGGTATTCGT 1242 0.500 57.2
rps16_p5 rps16 GTTGGTGATTAGGGTGGTGG GTTTTGGTCCCGGTATTCGT 1241 0.500 57.2
psbK-psbI_p1 psbK-psbI TGGCAAGCTGCTGTAAGTTT AACAAATAGTTTTAGAGTAAGCA 494–530 1.000 42.9
psbK-psbI_p2 psbK-psbI TTGGCAAGCTGCTGTAAGTT AACAAATAGTTTTAGAGTAAGCA 495–531 1.000 42.9
psbK-psbI_p3 psbK-psbI CTTTTGTTTGGCAAGCTGCT AACAAATAGTTTTAGAGTAAGCA 502–538 1.000 42.8
psbK-psbI_p4 psbK-psbI GTTTGGCAAGCTGCTGTAAG AACAAATAGTTTTAGAGTAAGCA 497–533 1.000 42.8
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT AACAAATAGTTTTAGAGTAAGCA 496–532 1.000 42.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGATATTAATCAACCCGGGGG 766–783 1.000 73.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGGATATTAATCAACCCGGGG 767–784 1.000 73.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGATATTAATCAACCCGGGGG 765–782 1.000 73.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGGATATTAATCAACCCGGGG 766–783 1.000 73.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA GGATATTAATCAACCCGGGGG 820–837 1.000 72.2
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 320–327 1.000 67.1
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 323–330 1.000 66.8
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 326–333 1.000 66.3
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 329–336 1.000 66.1
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 324–331 1.000 64.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Dendrocnide basirotunda NC_064737.1 152646 View on NCBI ↗
Dendrocnide meyeniana NC_064738.1 152621 View on NCBI ↗
Dendrocnide sinuata NC_064739.1 152650 View on NCBI ↗
Dendrocnide urentissima NC_064740.1 152658 View on NCBI ↗