Markers + reference

Elatostematoides

2 species · Urticaceae · Rosales

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Species 2
Genome length 155–156 kb
Candidate markers 272
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 281 0.0233 0.91 64.3 yes View details
petN-psbM LSC 740 0.0149 1.00 67.3 yes View details
trnL-UAA-trnF-GAA LSC 390 0.0181 0.99 58.3 yes View details
ndhC-trnV-UAC LSC 570 0.0105 1.00 64.2 yes View details
petG LSC 114 0.0000 1.00 21.3 yes View details
ycf1 IRb 1139 0.0009 1.00 59.3 no View details
ycf1-ndhF SSC 604 0.0033 1.00 48.2 yes View details
ccsA-ndhD SSC 269 0.0373 1.00 66.0 yes View details
ndhE SSC 306 0.0000 1.00 22.6 yes View details
ycf1 SSC 5469 0.0066 1.00 56.4 yes View details
petG-trnW-CCA LSC 111 0.1081 1.00 87.5 yes View details
ndhK-ndhC LSC 42 0.0238 1.00 66.2 yes View details
trnS-GCU-trnG-UCC LSC 734 0.0060 0.91 65.9 yes View details
trnK-UUU-rps16 LSC 829 0.0049 0.98 63.8 yes View details
trnC-GCA-petN LSC 925 0.0011 0.96 63.3 yes View details
rps16-trnQ-UUG LSC 736 0.0014 0.97 62.4 yes View details
accD-psaI LSC 671 0.0030 0.98 62.4 yes View details
petA-psbJ LSC 954 0.0063 1.00 62.4 yes View details
psbE-petL LSC 1210 0.0058 1.00 62.1 yes View details
rpl32-trnL-UAG SSC 958 0.0053 0.98 61.8 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 100 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 CCTCTAGACCTAGCTGCTGT 324–348 1.000 83.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 338–362 1.000 83.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 337–361 1.000 83.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 339–363 1.000 83.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 327–351 1.000 83.8
trnK-UUU_p1 trnK-UUU TGAAATGCGTTAATCGATTCCG TGGTTGCGCCGTACAATTTA 2814–2828 1.000 59.5
trnK-UUU_p2 trnK-UUU TGAAATGCGTTAATCGATTCCG GGTTGCGCCGTACAATTTAA 2813–2827 1.000 58.5
trnK-UUU_p3 trnK-UUU TGAAATGCGTTAATCGATTCCG AAAATGTTTTGGTTGCGCCG 2823–2837 1.000 54.9
trnK-UUU_p4 trnK-UUU TGAAATGCGTTAATCGATTCCG GGTTGCGCCGTACAATTTAAT 2813–2827 1.000 54.3
trnK-UUU_p5 trnK-UUU GAAATGCGTTAATCGATTCCG TGGTTGCGCCGTACAATTTA 2813–2827 1.000 54.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC ATTTCAAAGAAGGCGGGTGT 994–1001 1.000 81.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT ATTTCAAAGAAGGCGGGTGT 993–1000 1.000 81.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC AAAAGGCGCTCATCCTACAG 1028–1035 1.000 81.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT AAAAGGCGCTCATCCTACAG 1027–1034 1.000 81.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT TTGAAAAAGGCGCTCATCCT 1031–1038 1.000 80.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 796–809 1.000 80.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 811–824 1.000 78.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 810–823 1.000 78.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TGGGTGTAAGAATCCACAGC GAGGTTCGAATCCTTCCGTC 830–843 1.000 77.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGGTATTC 817–830 1.000 76.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AAGCTTTTGATCGGACTGGG 813–877 1.000 83.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AAGCTTTTGATCGGACTGGG 812–876 1.000 82.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AAGCTTTTGATCGGACTGGG 867–931 1.000 81.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GTCCACTCAGCCATCTTTCC AAGCTTTTGATCGGACTGGG 798–862 1.000 80.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC AAGCTTTTGATCGGACTGGG 815–879 1.000 80.1
trnC-GCA-petN_p1 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AGCCCAAGCGAGACTTACTA 1011–1046 1.000 81.3
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 955–990 1.000 81.3
trnC-GCA-petN_p3 trnC-GCA-petN GGGTGTCGCCTGATAAACAA AGCCCAAGCGAGACTTACTA 937–972 1.000 80.5
trnC-GCA-petN_p4 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AGAGTCCACTTCTTCCCCAT 1072–1107 1.000 79.6
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 1016–1051 1.000 79.5

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
Elatostematoides filicoides PQ676468.1 155639 View on NCBI ↗
Elatostematoides fruticulosa PQ676467.1 155075 View on NCBI ↗