Markers + reference

Elatostema

43 species · Urticaceae · Rosales

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Species 43
Genome length 149–164 kb
Candidate markers 270
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 765 0.0652 0.97 82.7 yes View details
ndhF-rpl32 SSC 874 0.0712 0.80 77.1 yes View details
ccsA-ndhD SSC 273 0.1005 1.00 75.4 yes View details
ycf1 SSC 5571 0.0820 0.85 72.7 yes View details
petA-psbJ LSC 915 0.0449 0.98 82.7 yes View details
trnK-UUU-rps16 LSC 775 0.0543 0.97 81.7 yes View details
trnS-GCU-trnG-UCC LSC 656 0.0428 0.98 81.1 yes View details
petN-psbM LSC 748 0.0437 0.99 80.2 yes View details
psbZ-trnG-GCC LSC 514 0.0423 0.92 79.8 yes View details
trnE-UUC-trnT-GGU LSC 547 0.0434 0.96 78.7 yes View details
accD-psaI LSC 691 0.0409 0.97 78.2 yes View details
trnT-UGU-trnL-UAA LSC 610 0.0420 1.00 77.9 yes View details
rpoB-trnC-GCA LSC 1052 0.0388 1.00 77.3 yes View details
ycf4-cemA LSC 741 0.0357 0.98 77.3 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC AAAAGGGTATGTTGCTGCCA 1545–1676 0.907 87.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT AAAAGGGTATGTTGCTGCCA 1544–1675 0.907 87.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT TTGAAAAAGGTGCTCAGCCT 873–1014 0.907 87.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC ATTTCAAAGAAGGCGGGTGT 852–977 0.279 59.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT ATTTCAAAGAAGGCGGGTGT 851–976 0.279 59.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 548–905 0.977 89.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 552–909 0.977 84.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 540–897 0.977 84.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 547–904 0.977 83.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 543–900 0.977 82.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCACT 408–759 0.953 80.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 407–758 0.953 80.2
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCAC 408–759 0.953 80.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCAC 407–758 0.953 80.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACGAATCGCACTTTTACCAC 409–760 0.953 77.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GATACCGGGGCTTTGCAATA ATTACCATCCCCGATTTGCC 2041–2116 0.186 54.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AGAGGTTCCCAGGGAATTCA ATTACCATCCCCGATTTGCC 1984–2059 0.186 54.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCGGGGCTTTGCAATATTTG ATTACCATCCCCGATTTGCC 2037–2112 0.186 54.0
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ACACGAACCCATATCCTTGC ATTACCATCCCCGATTTGCC 2160–2235 0.186 53.8
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCCTACTCACACGAACCCAT ATTACCATCCCCGATTTGCC 2168–2243 0.186 53.6
petN-psbM_p1 petN-psbM GGCAAATCGGGGATGGTAAT AATCATCAAACCGCCCTACC 1702–1795 0.186 54.9
petN-psbM_p2 petN-psbM GGCAAATCGGGGATGGTAAT TATAAACTAGTGCTCGCGCC 1751–1844 0.186 54.3
petN-psbM_p3 petN-psbM ATATGGCAAATCGGGGATGG AATCATCAAACCGCCCTACC 1786–1799 0.163 51.8
petN-psbM_p4 petN-psbM GGCAAATCGGGGATGGTAAT GCCCTACCGTTGCTTCTAAA 1772–1783 0.140 46.2
petN-psbM_p5 petN-psbM GGCAAATCGGGGATGGTAAT TCAAATCATCAAACCGCCCT 1787–1798 0.140 45.3
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA ACGCCTTACCATGACGTTAC 342–629 1.000 90.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA ACGCCTTACCATGACGTTAC 340–627 1.000 90.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GATGTCCTGAACCGCTAGAC ACGCCTTACCATGACGTTAC 339–626 1.000 90.3
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 355–642 0.953 88.9
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 353–640 0.953 88.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (43)

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

Species Accession Length (bp) Link
Elatostema acutidentatum OR521107.1 153693 View on NCBI ↗
Elatostema austrosinense OR521108.1 153635 View on NCBI ↗
Elatostema brachyodontum PQ676442.1 151222 View on NCBI ↗
Elatostema brevifolium OR521104.1 153419 View on NCBI ↗
Elatostema calcareum PQ676451.1 151197 View on NCBI ↗
Elatostema caulialatum OR521100.1 153525 View on NCBI ↗
Elatostema dissectum NC_047192.1 150302 View on NCBI ↗
Elatostema goudotianum PQ676460.1 154132 View on NCBI ↗
Elatostema grande PQ676448.1 149710 View on NCBI ↗
Elatostema grandifolium PQ676449.1 149742 View on NCBI ↗
Elatostema grijsii PQ676465.1 154282 View on NCBI ↗
Elatostema gyrocephalum PQ676441.1 163566 View on NCBI ↗
Elatostema hechiense PQ676439.1 163669 View on NCBI ↗
Elatostema heterolobum OR521101.1 153732 View on NCBI ↗
Elatostema hezhouense PQ676445.1 150624 View on NCBI ↗
Elatostema hypoglaucum PQ676437.1 150784 View on NCBI ↗
Elatostema incisum PQ676461.1 154152 View on NCBI ↗
Elatostema laevissimum PQ676457.1 150966 View on NCBI ↗
Elatostema laevissimum var. laevissimum MN189961.1 150244 View on NCBI ↗
Elatostema lineolatum var. major PQ722561.1 150292 View on NCBI ↗
Elatostema lithoneurum PQ676447.1 150601 View on NCBI ↗
Elatostema lutescens PQ676450.1 151315 View on NCBI ↗
Elatostema macintyrei PQ676456.1 150808 View on NCBI ↗
Elatostema madagascariense PQ676462.1 154050 View on NCBI ↗
Elatostema monandrum PQ676459.1 149152 View on NCBI ↗
Elatostema nasutum PQ676458.1 150034 View on NCBI ↗
Elatostema oblongifolium PQ676471.1 164018 View on NCBI ↗
Elatostema orientale PQ676463.1 154097 View on NCBI ↗
Elatostema parvum NC_064741.1 153091 View on NCBI ↗
Elatostema paucidentatum OR521102.1 153547 View on NCBI ↗
Elatostema platyphyllum PQ676435.1 150675 View on NCBI ↗
Elatostema qinzhouense MW172521.1 150398 View on NCBI ↗
Elatostema radicans PQ676433.1 154159 View on NCBI ↗
Elatostema rugosum PQ676454.1 151006 View on NCBI ↗
Elatostema serra PQ676453.1 150866 View on NCBI ↗
Elatostema sinense var. longicornutum PQ676466.1 152759 View on NCBI ↗
Elatostema stewardii NC_061041.1 150263 View on NCBI ↗
Elatostema subcoriaceum PQ676472.1 150737 View on NCBI ↗
Elatostema suzukii PQ676452.1 150817 View on NCBI ↗
Elatostema tianeense PQ676444.1 150527 View on NCBI ↗
Elatostema villosum PQ676438.1 150656 View on NCBI ↗
Elatostema welwitschii PQ676455.1 150252 View on NCBI ↗
Elatostema yachense PQ676446.1 150347 View on NCBI ↗