Markers + reference

Kuepferia

3 species · Gentianaceae · Gentianales

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Species 3
Genome length 137–143 kb
Candidate markers 268
Primer pairs 95

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 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-trnQ-UUG LSC 1569 0.0515 0.43 64.1 yes View details
atpH-atpI LSC 866 0.0480 0.99 82.9 yes View details
rpoB-trnC-GCA LSC 862 0.0391 0.98 74.1 yes View details
ndhC-trnV-UAC LSC 308 0.2019 0.91 74.9 yes View details
rbcL-accD LSC 690 0.0856 0.86 80.9 yes View details
rps12-trnV-GAC IRb 1025 0.0352 0.97 67.0 yes View details
trnR-ACG-trnN-GUU IRb 276 0.3086 0.98 79.5 yes View details
trnN-GUU-trnR-ACG IRa 276 0.3049 0.98 79.5 yes View details
trnV-GAC-rps12 IRa 1025 0.0359 0.97 67.4 yes View details
psbL-psbF LSC 23 0.0580 1.00 76.7 yes View details
petB-petD LSC 199 0.0842 0.99 76.1 yes View details
rpl32-trnL-UAG SSC 593 0.0411 1.00 74.4 yes View details
trnT-UGU-trnL-UAA LSC 715 0.0333 0.90 73.4 yes View details
trnG-GCC-trnfM-CAU LSC 133 0.0602 1.00 72.8 yes View details
rpl14-rpl16 LSC 101 0.0594 1.00 72.0 yes View details
petL-petG LSC 169 0.0375 1.00 71.5 yes View details
infA LSC 237 0.0378 0.97 70.7 yes View details
ndhG-ndhI SSC 390 0.0364 0.99 70.2 yes View details
ndhF-rpl32 SSC 661 0.0318 0.98 69.9 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG CGAATCCCTTGCTTCATCCA AGCAGCTTGCCAAACAAAAG 1220–2237 1.000 86.3
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG CGAATCCCTTGCTTCATCCA CTTACAGCAGCTTGCCAAAC 1225–2242 1.000 86.3
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG ACGAATCCCTTGCTTCATCC AGCAGCTTGCCAAACAAAAG 1221–2238 1.000 86.3
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG GGACGAATCCCTTGCTTCAT AGCAGCTTGCCAAACAAAAG 1223–2240 1.000 86.3
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG ATGGACGAATCCCTTGCTTC AGCAGCTTGCCAAACAAAAG 1225–2242 1.000 86.2
atpH-atpI_p1 atpH-atpI AAGCAAGTCCTACAGCCAAC TAGGTGAATCCATGGAAGGC 821–985 1.000 80.0
atpH-atpI_p2 atpH-atpI CAGCAGCAATAACAGAAGCG TAGGTGAATCCATGGAAGGC 800–964 1.000 79.6
atpH-atpI_p3 atpH-atpI GAAGCAAGTCCTACAGCCAA TAGGTGAATCCATGGAAGGC 822–986 1.000 79.3
atpH-atpI_p4 atpH-atpI AAGCAAGTCCTACAGCCAAC GGTGAATCCATGGAAGGCC 819–983 1.000 78.7
atpH-atpI_p5 atpH-atpI CAGCAGCAATAACAGAAGCG GGTGAATCCATGGAAGGCC 798–962 1.000 78.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT TTTTATCAGCCGACGAAGGG 1483–1744 1.000 86.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG TTTTATCAGCCGACGAAGGG 1675–1936 1.000 86.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG CATTTCCTACCAGGCTGTCC 1891–2161 0.667 69.6
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG CCATTTCCTACCAGGCTGTC 1892–2162 0.667 69.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TAGACACTCCCTCATTGCCA TTTTATCAGCCGACGAAGGG 1002 0.333 52.8
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU GTTCGATTCCCGCTATCCG CTTGAGGTCACGGGTTCAAA 162–252 1.000 78.6
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU GGTTCGATTCCCGCTATCC CTTGAGGTCACGGGTTCAAA 163–253 1.000 78.4
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU GTTCGATTCCCGCTATCCG GGGTAGAGCAGTTTGGTAGC 198–288 1.000 78.0
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU GGGTTCGATTCCCGCTATC GGGTAGAGCAGTTTGGTAGC 200–290 1.000 77.8
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU GGTTCGATTCCCGCTATCC GGGTAGAGCAGTTTGGTAGC 199–289 1.000 77.8
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 652–765 1.000 86.4
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 660–773 1.000 85.9
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA TAGGAAAAAGCCGGCTATCG ACCAATTTCGCCATATCCCC 703–816 1.000 85.4
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 684–797 1.000 85.4
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA TAGGAAAAAGCCGGCTATCG TAGCGTCTACCAATTTCGCC 711–824 1.000 84.8
ndhC-trnV-UAC_p1 ndhC-trnV-UAC GGGGCTAAAACTCCGGAAAT GGTTCGAATCCGTATAGCCC 375–428 1.000 90.3
ndhC-trnV-UAC_p2 ndhC-trnV-UAC AATTGGGGCTAAAACTCCGG GGTTCGAATCCGTATAGCCC 379–432 1.000 90.2
ndhC-trnV-UAC_p3 ndhC-trnV-UAC TCTCACTAAAGAAGGGGCCA GGTTCGAATCCGTATAGCCC 967–1014 0.667 73.9
ndhC-trnV-UAC_p4 ndhC-trnV-UAC TCTCACTAAAGAAGGGGCCA GGTCTGATTGTAGTGCCGTT 1451–1497 0.667 72.6
ndhC-trnV-UAC_p5 ndhC-trnV-UAC TCTCACTAAAGAAGGGGCCA AGGGCTATAGCTCAGTTGGT 1615–1655 0.667 71.6

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
Kuepferia damyonensis MN199133.1 142894 View on NCBI ↗
Kuepferia decorata MN199130.1 136801 View on NCBI ↗
Kuepferia otophora NC_051950.1 139976 View on NCBI ↗