Markers + reference

Triosteum

4 species · Caprifoliaceae · Dipsacales

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Species 4
Genome length 154–157 kb
Candidate markers 269
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rbcL-accD LSC 1699 0.1935 0.67 75.5 yes View details
accD LSC 1644 0.0870 0.95 83.0 yes View details
trnP-GGG-psaJ LSC 495 0.0734 0.98 83.5 yes View details
trnN-GUU-ndhF IRb 842 0.0818 1.00 85.1 yes View details
ycf1-trnN-GUU IRa 1072 0.2520 0.96 81.6 yes View details
trnN-GUU-trnR-ACG IRa 205 0.1561 1.00 73.6 yes View details
psaA-ycf3 LSC 770 0.0284 0.99 82.4 yes View details
trnG-GCC-trnR-UCU LSC 174 0.0460 1.00 78.4 yes View details
accD-psaI LSC 732 0.0454 0.98 77.7 yes View details
ndhK-ndhC LSC 60 0.0361 0.97 72.6 yes View details
ycf4-cemA LSC 953 0.0140 0.99 70.5 yes View details
rpl32-trnL-UAG SSC 804 0.0252 0.99 69.2 yes View details
trnF-GAA-ndhJ LSC 709 0.0128 0.99 69.1 yes View details
infA-rps8 LSC 189 0.0549 0.78 68.9 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 245–257 1.000 71.8
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 248–260 1.000 71.5
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 251–263 1.000 71.0
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 254–266 1.000 70.8
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 249–261 1.000 69.3
psaA-ycf3_p1 psaA-ycf3 TGAGAAATGACCGGGTTTGG ATCAAGCCGCTGAGTATTGG 961–979 1.000 84.8
psaA-ycf3_p2 psaA-ycf3 TGAGAAATGACCGGGTTTGG GGAAACAGGCTATAGCGCTT 943–961 1.000 84.8
psaA-ycf3_p3 psaA-ycf3 GCCCATTCCTCGAAAGAAGT GGAAACAGGCTATAGCGCTT 924–942 1.000 84.8
psaA-ycf3_p4 psaA-ycf3 TGAGAAATGACCGGGTTTGG TTGGTTGAAGATCACCAGGC 894–912 1.000 84.8
psaA-ycf3_p5 psaA-ycf3 GCCCATTCCTCGAAAGAAGT ATCAAGCCGCTGAGTATTGG 942–960 1.000 84.7
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA TGGATAGGATGGCCTTTACG 837–853 1.000 72.8
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA GGATAGGATGGCCTTTACGT 836–852 1.000 72.8
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA TGGATAGGATGGCCTTTACG 801–817 1.000 72.6
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA GGATAGGATGGCCTTTACGT 800–816 1.000 72.6
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ CTGGTAGAGCAGAGGACTGA TGGATAGGATGGCCTTTACG 825–841 1.000 71.8
ndhK-ndhC_p1 ndhK-ndhC ACCATAGAGAAGCGGCCATA AAAAGGGGCATTGGAATGGT 201–207 1.000 80.9
ndhK-ndhC_p2 ndhK-ndhC ACCATAGAGAAGCGGCCATA GGTTCAGTTTATGCATGGCG 221–227 1.000 79.4
ndhK-ndhC_p3 ndhK-ndhC ACCATAGAGAAGCGGCCATA CGAAAAGGGGCATTGGAATG 203–209 1.000 78.8
ndhK-ndhC_p4 ndhK-ndhC ACCATAGAGAAGCGGCCATA TGGGCAATGAGTTTCGATGT 296–302 1.000 78.6
ndhK-ndhC_p5 ndhK-ndhC ACCATAGAGAAGCGGCCATA AAAGGGGCATTGGAATGGTC 200–206 1.000 77.9
rbcL-accD_p1 rbcL-accD GCACGACTACTTAACAGGGG CTGAAAGCGAGACCACTACC 1855–2569 1.000 91.9
rbcL-accD_p2 rbcL-accD CGTAGCTAATCGAGTCGCTC CTGAAAGCGAGACCACTACC 1402–2116 1.000 91.5
rbcL-accD_p3 rbcL-accD GCTCTGACCGAGATCTTTGG CTGAAAGCGAGACCACTACC 1488–2202 1.000 91.4
rbcL-accD_p4 rbcL-accD AGATTGGGTCTCTCTACCGG CTGAAAGCGAGACCACTACC 1555–2269 1.000 91.4
rbcL-accD_p5 rbcL-accD GCACGACTACTTAACAGGGG ACAAGAACAACACTGCCCAT 1672–2386 0.500 66.0
accD_p1 accD GGTAGTGGTCTCGCTTTCAG CCCATTGCTACGGGAATACC 923–2114 0.750 81.1
accD_p2 accD ACAGGTCTACAGGGGTACAC CCATTGCAATTGCCGGAAAT 2780 0.250 49.3
accD_p3 accD GTTACAGGGGTACAGGGCTA CCATTGCAATTGCCGGAAAT 2971 0.250 48.7
accD_p4 accD TTACAGGGGTACAGGGCTAC CCATTGCAATTGCCGGAAAT 2970 0.250 48.7
accD_p5 accD ACAGGTCTACAGGGGTACAC CGGGAGGAGGAAATTCGTTT 2244 0.250 48.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Triosteum himalayanum NC_045219.1 154579 View on NCBI ↗
Triosteum perfoliatum PQ559727.1 154477 View on NCBI ↗
Triosteum pinnatifidum NC_037952.1 154896 View on NCBI ↗
Triosteum sinuatum NC_068129.1 157178 View on NCBI ↗