Markers + reference

Triplostegia

2 species · Caprifoliaceae · Dipsacales

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Species 2
Genome length 156–158 kb
Candidate markers 263
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpH-atpI LSC 1172 0.0180 0.99 69.6 yes View details
ycf2 IRb 7192 0.0052 0.96 44.3 no View details
ycf2-trnL-CAA IRb 624 0.1692 0.83 80.4 yes View details
trnN-GUU-ndhF SSC 1370 0.2808 0.84 83.3 yes View details
ycf1 SSC 5466 0.0534 0.84 82.3 yes View details
trnL-CAA-ycf2 IRa 623 0.1676 0.83 80.3 yes View details
ycf2 IRa 7191 0.0054 0.96 44.7 yes View details
trnI-CAU-trnH-GUG LSC 46 0.1087 1.00 87.5 no View details
accD-psaI LSC 572 0.0113 0.93 68.8 yes View details
rpl22 LSC 603 0.0149 0.78 67.0 yes View details
rps2-rpoC2 LSC 302 0.0232 1.00 65.9 yes View details
petN-psbM LSC 1205 0.0060 0.96 65.9 yes View details
psaJ-rpl33 LSC 497 0.0064 0.95 65.0 yes View details
rps16-trnQ-UUG LSC 1769 0.0030 0.94 64.6 yes View details
trnE-UUC-trnT-GGU LSC 827 0.0113 0.96 64.0 yes View details
rbcL-accD LSC 901 0.0071 0.93 63.7 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AGAGCACCCTCATTCCGATA TCGGAGGTTCGAATCCTTTC 1817–1913 1.000 78.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AGAGCACCCTCATTCCGATA TAAGGCAACGGGTTTTGGTC 1844–1940 1.000 78.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TCGGAGGTTCGAATCCTTTC 1749–1845 1.000 77.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1776–1872 1.000 77.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGAGCACCCTCATTCCGATA GGGTTTTGGTCCCGCTATTC 1835–1931 1.000 76.3
atpH-atpI_p1 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTTGCAACTTTAGCCGCG 1271–1276 1.000 76.4
atpH-atpI_p2 atpH-atpI CAGCAGCAATAACAGAAGCG TTTTTGCAACTTTAGCCGCG 1263–1268 1.000 76.2
atpH-atpI_p3 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTTGCAACTTTAGCCGCG 1270–1275 1.000 75.8
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA CCGCGGCTTATATAGGTGAA 1256–1261 1.000 74.6
atpH-atpI_p5 atpH-atpI CAGCAGCAATAACAGAAGCG CCGCGGCTTATATAGGTGAA 1248–1253 1.000 74.5
rps2-rpoC2_p1 rps2-rpoC2 AACTCCTGCCTCCATCATCT ATTAGTGCACCCTTCAAGGC 462 1.000 79.1
rps2-rpoC2_p2 rps2-rpoC2 TGCCTCCATCATCTCTTCCA ATTAGTGCACCCTTCAAGGC 456 1.000 79.0
rps2-rpoC2_p3 rps2-rpoC2 AACTCCTGCCTCCATCATCT TTCGAGGGGGAAATGAGAGA 401 1.000 78.5
rps2-rpoC2_p4 rps2-rpoC2 TGCCTCCATCATCTCTTCCA TTCGAGGGGGAAATGAGAGA 395 1.000 78.5
rps2-rpoC2_p5 rps2-rpoC2 TCCTGCCTCCATCATCTCTT ATTAGTGCACCCTTCAAGGC 459 1.000 78.4
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT CTAGTCCCTACCGCCTTTCT 1302–1348 1.000 80.2
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TCTAGTCCCTACCGCCTTTC 1303–1349 1.000 80.2
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TCCCTACCGCCTTTCTACTT 1298–1344 1.000 80.1
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT TTCTAGTCCCTACCGCCTTT 1304–1350 1.000 80.0
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT CATTCTAGTCCCTACCGCCT 1306–1352 1.000 79.6
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 904–914 1.000 82.6
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 902–912 1.000 82.6
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 883–893 1.000 82.2
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 881–891 1.000 82.2
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU AACTTCCTTTCGCAGTACCC GAACCGATGACTTACGCCTT 965–975 1.000 82.1
rbcL-accD_p1 rbcL-accD GCGTTGGAGAGATCGTTTCT TGCTTGTATGAGGGAGTGGA 2416–2998 1.000 84.1
rbcL-accD_p2 rbcL-accD GCACGACTACTTAACAGGGG TGCTTGTATGAGGGAGTGGA 2254–2836 1.000 84.1
rbcL-accD_p3 rbcL-accD AATGAGGGACGTGATCTTGC TGCTTGTATGAGGGAGTGGA 1758–2340 1.000 84.0
rbcL-accD_p4 rbcL-accD ATGAAATTATCCGTGCGGCT TGCTTGTATGAGGGAGTGGA 1727–2309 1.000 84.0
rbcL-accD_p5 rbcL-accD GGTAGCTGCCGAATCTTCAA TCTCATCGCAACTCCGAATG 2529–2610 1.000 83.5

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
Triplostegia glandulifera NC_045051.1 157560 View on NCBI ↗
Triplostegia grandiflora NC_072070.1 155705 View on NCBI ↗