Markers + reference

Strophanthus

3 species · Apocynaceae · Gentianales

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Species 3
Genome length 155–156 kb
Candidate markers 265
Primer pairs 100

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 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 764 0.0198 0.97 66.9 yes View details
rps16-trnQ-UUG LSC 1283 0.0189 0.99 71.0 yes View details
atpH-atpI LSC 1150 0.0203 1.00 65.6 yes View details
rpoB-trnC-GCA LSC 1268 0.0179 1.00 74.7 yes View details
psbM-trnD-GUC LSC 875 0.0162 0.99 62.5 yes View details
trnP-UGG-psaJ LSC 376 0.0523 0.97 77.2 yes View details
rpl32-trnL-UAG SSC 917 0.0220 0.99 64.7 yes View details
psaC SSC 246 0.0081 1.00 46.1 yes View details
ycf1 SSC 5493 0.0141 1.00 51.0 yes View details
ndhC-trnV-UAC LSC 1141 0.0171 0.97 73.7 yes View details
ccsA-ndhD SSC 252 0.0159 1.00 66.3 yes View details
rps4-trnT-UGU LSC 389 0.0209 0.98 66.1 yes View details
trnS-GCU-trnG-UCC LSC 541 0.0168 0.99 65.7 yes View details
psaI-ycf4 LSC 442 0.0128 1.00 65.7 yes View details
ycf3-trnS-GGA LSC 521 0.0141 1.00 64.5 yes View details
trnH-GUG-psbA LSC 336 0.0242 0.99 64.3 yes View details
trnF-GAA-ndhJ LSC 691 0.0131 0.96 64.0 yes View details
ndhF-rpl32 SSC 807 0.0134 0.98 61.1 yes View details
matK-trnK-UUU LSC 697 0.0177 1.00 61.0 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 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 390–418 1.000 84.0
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 393–421 1.000 83.9
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 404–432 1.000 83.8
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 403–431 1.000 83.8
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 405–433 1.000 83.7
trnK-UUU_p1 trnK-UUU ACGGATTTCTATACATATAATTTCGA TCTTCTATAGTTGGTTTCTTCTT 2610–2613 1.000 41.3
trnK-UUU_p2 trnK-UUU ACGGATTTCTATACATATAATTTCGA TCTTCTATAGTTGGTTTCTTCTTT 2610–2613 1.000 41.3
trnK-UUU_p3 trnK-UUU ACGGATTTCTATACATATAATTTCGA ATCTTCTATAGTTGGTTTCTTCT 2611–2614 1.000 41.3
trnK-UUU_p4 trnK-UUU ACGGATTTCTATACATATAATTTCG TCTTCTATAGTTGGTTTCTTCTT 2610–2613 1.000 41.3
trnK-UUU_p5 trnK-UUU ACGGATTTCTATACATATAATTTCGA TCTTCTATAGTTGGTTTCTTCTTTTC 2610–2613 1.000 41.3
matK-trnK-UUU_p1 matK-trnK-UUU ATGGTCATGAGCAAGTGCAT AACGGTAGAGTACTCGGCTT 824–827 1.000 79.5
matK-trnK-UUU_p2 matK-trnK-UUU ATGGTCATGAGCAAGTGCAT ACGGTAGAGTACTCGGCTTT 823–826 1.000 79.5
matK-trnK-UUU_p3 matK-trnK-UUU ATGGTCATGAGCAAGTGCAT GGGTTGCTAACTCAACGGTA 837–840 1.000 77.1
matK-trnK-UUU_p4 matK-trnK-UUU ATGGTCATGAGCAAGTGCAT TTCGGGTTGCTAACTCAACG 840–843 1.000 76.8
matK-trnK-UUU_p5 matK-trnK-UUU TGGTCATGAGCAAGTGCATA ACGGTAGAGTACTCGGCTTT 822–825 1.000 74.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCAAAGGGTGGGGGTTTTT 884–915 1.000 82.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTTCAAAGGGTGGGGGTTTT 885–916 1.000 82.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTTTCAAAGGGTGGGGGTTT 886–917 1.000 82.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTTTTCAAAGGGTGGGGGTT 887–918 1.000 82.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCAAAGGGTGGGGGTTTTT 822–853 1.000 81.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1343–1365 1.000 82.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1354–1376 1.000 82.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1347–1369 1.000 77.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1373–1395 1.000 77.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 1355–1377 1.000 77.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA TCAAACCGAAAACAAAGACCC 647–660 1.000 68.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA CAAACCGAAAACAAAGACCCT 646–659 1.000 68.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TCAAGTCATCAAGGGAAGCG TCAAACCGAAAACAAAGACCC 713–726 1.000 67.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TCAAGTCATCAAGGGAAGCG CAAACCGAAAACAAAGACCCT 712–725 1.000 67.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CATCAAGGGAAGCGGAAAGA TCAAACCGAAAACAAAGACCC 707–720 1.000 67.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Strophanthus divaricatus PV798297.1 155409 View on NCBI ↗
Strophanthus hispidus NC_079589.1 155522 View on NCBI ↗
Strophanthus wallichii NC_079590.1 155602 View on NCBI ↗