Markers + reference

Tripterospermum

5 species · Gentianaceae · Gentianales

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Species 5
Genome length 151–151 kb
Candidate markers 267
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psaA-ycf3 LSC 831 0.0039 1.00 51.5 yes View details
trnT-UGU-trnL-UAA LSC 690 0.0038 0.99 56.8 yes View details
trnF-GAA-ndhJ LSC 552 0.0053 0.95 51.0 yes View details
rbcL LSC 1458 0.0027 1.00 47.5 yes View details
accD-psaI LSC 536 0.0046 0.98 38.5 yes View details
psaJ-rpl33 LSC 499 0.0029 0.82 43.1 yes View details
rpl16 LSC 1191 0.0012 0.99 41.4 yes View details
rrn4.5-rrn5 IRb 244 0.0213 1.00 52.6 yes View details
rrn5-trnR-ACG IRb 261 0.0015 1.00 38.7 yes View details
rpl32-trnL-UAG SSC 822 0.0061 0.98 52.7 yes View details
ycf1 SSC 5508 0.0027 1.00 42.8 yes View details
trnR-ACG-rrn5 IRa 261 0.0015 1.00 38.7 yes View details
rrn5-rrn4.5 IRa 244 0.0213 1.00 52.6 yes View details
rpl2-trnH-GUG IRa 250 0.0016 1.00 70.6 no View details
psbE-petL LSC 1033 0.0036 0.97 63.8 yes View details
rpoB-trnC-GCA LSC 1292 0.0026 0.97 58.7 yes View details
petA-psbJ LSC 593 0.0049 0.99 57.3 yes View details
ndhC-trnV-UAC LSC 826 0.0010 0.94 55.9 yes View details
trnC-GCA-petN LSC 736 0.0023 1.00 55.5 yes View details
rpoA LSC 1011 0.0030 1.00 53.5 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
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GTTCTTCCGTCAAACCCTCA TTTTATCAGCCGACGAAGGG 1402–1506 1.000 82.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTTCTTCCGTCAAACCCTCA CCGGATTTGAACTGGGGAAA 1354–1457 1.000 81.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GTTCTTCCGTCAAACCCTCA GACGAAGGGATTTCAAGGCT 1391–1495 1.000 81.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CTTCCGTCAAACCCTCATCA TTTTATCAGCCGACGAAGGG 1399–1503 1.000 80.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GTTCTTCCGTCAAACCCTCA GGTACCCGGATTTGAACTGG 1359–1462 1.000 80.4
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 581–799 1.000 83.7
trnC-GCA-petN_p2 trnC-GCA-petN CCCAGTTCAAATCCGGGTAC TTAAAGCAGCCCAAGCAAGA 577–795 1.000 82.3
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 575–793 1.000 82.2
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TTAAAGCAGCCCAAGCAAGA 599–817 1.000 81.5
trnC-GCA-petN_p5 trnC-GCA-petN CCCAGTTCAAATCCGGGTAC CAGCCCAAGCAAGACTTACT 571–789 1.000 80.9
psaA-ycf3_p1 psaA-ycf3 TTTTACTTCTGGTTCCGGCG ATCAAGCCGCTGAGTATTGG 962–972 1.000 78.3
psaA-ycf3_p2 psaA-ycf3 TGTTCTTGAGAAATGGCCCG ATCAAGCCGCTGAGTATTGG 1034–1044 1.000 78.2
psaA-ycf3_p3 psaA-ycf3 TTTTACTTCTGGTTCCGGCG TTGAAGATCACGAGGCGTTT 891–901 1.000 77.5
psaA-ycf3_p4 psaA-ycf3 TGTTCTTGAGAAATGGCCCG TTGAAGATCACGAGGCGTTT 963–973 1.000 77.4
psaA-ycf3_p5 psaA-ycf3 TGTTCTTGAGAAATGGCCCG TTGGTTGAAGATCACGAGGC 967–977 1.000 77.2
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA AGGGGCAGTTTCAATCATGG ACCAATTTCGCCATATCCCC 820–830 1.000 80.6
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GGGGCAGTTTCAATCATGGA ACCAATTTCGCCATATCCCC 819–829 1.000 80.5
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA AGGGGCAGTTTCAATCATGG TAGCGTCTACCAATTTCGCC 828–838 1.000 80.0
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGGGCAGTTTCAATCATGGA TAGCGTCTACCAATTTCGCC 827–837 1.000 80.0
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA TAGGAAAAAGCCGGCTATCG ACCAATTTCGCCATATCCCC 786–796 1.000 79.9
trnL-UAA_p1 trnL-UAA CGGAGCGACCTCACAATAAA TAGGCTAAAGGGTCGGGAAA 543–675 1.000 85.1
trnL-UAA_p2 trnL-UAA CGGAGCGACCTCACAATAAA GGTCAGGTGCATCAGGAATT 592–724 1.000 84.3
trnL-UAA_p3 trnL-UAA CGGAGCGACCTCACAATAAA AATTGGTCAGGTGCATCAGG 596–728 1.000 84.1
trnL-UAA_p4 trnL-UAA CGGAGCGACCTCACAATAAA AAGGGGGATAGGCTAAAGGG 551–683 1.000 84.1
trnL-UAA_p5 trnL-UAA CGGAGCGACCTCACAATAAA ATAGGCTAAAGGGTCGGGAA 544–676 1.000 84.0
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA CCGGAAAGTTGGATAGGGTG 690–700 1.000 83.6
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA CGGAAAGTTGGATAGGGTGG 689–699 1.000 83.6
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA CGGAAAGTTGGATAGGGTGG 653–663 1.000 83.4
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ GGATGCTACATTGGGACTGG CCGGAAAGTTGGATAGGGTG 712–722 1.000 83.3
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ GGATGCTACATTGGGACTGG CGGAAAGTTGGATAGGGTGG 711–721 1.000 83.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Tripterospermum championii MN199139.1 151350 View on NCBI ↗
Tripterospermum filicaule NC_087978.1 151215 View on NCBI ↗
Tripterospermum luteoviride MN199144.1 150929 View on NCBI ↗
Tripterospermum membranaceum NC_051951.1 151218 View on NCBI ↗
Tripterospermum nienkui NC_087979.1 151100 View on NCBI ↗