Markers + reference

Dipsacus

3 species · Caprifoliaceae · Dipsacales

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Species 3
Genome length 160–161 kb
Candidate markers 271
Primer pairs 85

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 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps2 LSC 711 0.0000 1.00 26.0 yes View details
psbM-trnD-GUC LSC 935 0.0093 1.00 64.7 yes View details
rbcL-accD LSC 1334 0.0100 1.00 65.6 yes View details
psbE-petL LSC 1034 0.0032 1.00 57.5 yes View details
clpP LSC 2103 0.0035 1.00 45.0 yes View details
ycf1 IRb 1956 0.0048 0.99 50.3 yes View details
ccsA SSC 966 0.0041 1.00 40.5 yes View details
ccsA-ndhD SSC 249 0.0215 1.00 52.1 yes View details
ycf1 SSC 5721 0.0036 1.00 27.8 no View details
rps2-rpoC2 LSC 186 0.0179 1.00 63.9 yes View details
trnG-GCC-trnfM-CAU LSC 184 0.0109 1.00 60.0 yes View details
atpH-atpI LSC 1183 0.0011 1.00 59.6 yes View details
petA-psbJ LSC 998 0.0013 1.00 59.6 yes View details
ycf4-cemA LSC 944 0.0021 1.00 56.4 yes View details
rpoB-trnC-GCA LSC 1302 0.0010 1.00 55.8 yes View details
cemA LSC 690 0.0048 1.00 55.1 yes View details
rps15-ycf1 SSC 399 0.0033 1.00 53.2 yes View details
rpoC2 LSC 4203 0.0010 1.00 51.5 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
atpH-atpI_p1 atpH-atpI GCCAACTCCAGGTCCAATAG TTTTTGCAACTTTAGCCGCG 1320 1.000 75.7
atpH-atpI_p2 atpH-atpI GCCAACTCCAGGTCCAATAG CAAGCGGGATTCAAGCTCTT 1341 1.000 75.5
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTTGCAACTTTAGCCGCG 1287 1.000 74.9
atpH-atpI_p4 atpH-atpI CAGCAGCAATAACAGAAGCG TTTTTGCAACTTTAGCCGCG 1279 1.000 74.7
atpH-atpI_p5 atpH-atpI AGCCAATCCAGCAGCAATAA CAAGCGGGATTCAAGCTCTT 1308 1.000 74.7
rps2_p1 rps2 CCCTTTTGCTAAGACCTGCA GTACACCCTTCAAGGCAACA 1785 1.000 79.3
rps2_p2 rps2 AGAAATTCTGACTGCCGGTC GTACACCCTTCAAGGCAACA 1530 1.000 79.3
rps2_p3 rps2 TTCTACGCCGGATATCTCGT GTACACCCTTCAAGGCAACA 1379 1.000 79.2
rps2_p4 rps2 GGACTTGGAAACCGCCTATT GTACACCCTTCAAGGCAACA 1422 1.000 79.1
rps2_p5 rps2 CCCTTTTGCTAAGACCTGCA GATACGCCGGAACAATCAGT 1653 1.000 79.0
rps2-rpoC2_p1 rps2-rpoC2 CCATGGCCAAAATGAACTCC GATACGCCGGAACAATCAGT 332 1.000 75.3
rps2-rpoC2_p2 rps2-rpoC2 CCATGGCCAAAATGAACTCC TACGATACGCCGGAACAATC 335 1.000 74.8
rps2-rpoC2_p3 rps2-rpoC2 GCCAAAATGAACTCCTGCCT GATACGCCGGAACAATCAGT 327 1.000 74.8
rps2-rpoC2_p4 rps2-rpoC2 CCATGGCCAAAATGAACTCC CTACGATACGCCGGAACAAT 336 1.000 74.7
rps2-rpoC2_p5 rps2-rpoC2 GCCAAAATGAACTCCTGCCT TACGATACGCCGGAACAATC 330 1.000 74.3
rpoC2_p1 rpoC2 CCCATTTCGAGGACTCACAG GACCCCCAAGGACAAATGAT 237 1.000 76.3
rpoC2_p2 rpoC2 CCCATTTCGAGGACTCACAG GAGGATTAATGTCGGACCCC 251 1.000 76.1
rpoC2_p3 rpoC2 TCACAGAAATACCTTGGGCG GACCCCCAAGGACAAATGAT 223 1.000 75.6
rpoC2_p4 rpoC2 TCACAGAAATACCTTGGGCG GAGGATTAATGTCGGACCCC 237 1.000 75.4
rpoC2_p5 rpoC2 CCCATTTCGAGGACTCACAG GATTAATGTCGGACCCCCAA 248 1.000 74.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CATCAAGCCCTGCTCAATGA CCGGATTTGAACTGGGGAAA 1460–1461 1.000 77.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCCCTCATTTCCATCCTGGA CCGGATTTGAACTGGGGAAA 1388–1389 1.000 77.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GTCCCTCATTTCCATCCTGG CCGGATTTGAACTGGGGAAA 1389–1390 1.000 76.6
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCAAGCCCTGCTCAATGAAC CCGGATTTGAACTGGGGAAA 1458–1459 1.000 75.8
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AAAGTTCGTCCATCAAGCCC CCGGATTTGAACTGGGGAAA 1470–1471 1.000 75.7
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAAAGGCGGTAGGGACTAG GCTAGATCCCCTCTTTCCCT 1094–1106 1.000 78.3
psbM-trnD-GUC_p2 psbM-trnD-GUC GAAAGGCGGTAGGGACTAGA GCTAGATCCCCTCTTTCCCT 1093–1105 1.000 78.2
psbM-trnD-GUC_p3 psbM-trnD-GUC AAAGGCGGTAGGGACTAGAA GCTAGATCCCCTCTTTCCCT 1092–1104 1.000 78.1
psbM-trnD-GUC_p4 psbM-trnD-GUC AAGTAGAAAGGCGGTAGGGA GCTAGATCCCCTCTTTCCCT 1098–1110 1.000 78.1
psbM-trnD-GUC_p5 psbM-trnD-GUC AGGCGGTAGGGACTAGAATG GCTAGATCCCCTCTTTCCCT 1090–1102 1.000 77.7

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
Dipsacus asper NC_039748.1 160530 View on NCBI ↗
Dipsacus asperoides NC_064366.1 160723 View on NCBI ↗
Dipsacus japonicus NC_039668.1 160371 View on NCBI ↗