Markers + reference

Heliophila

16 species · Brassicaceae · Brassicales

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Species 16
Genome length 153–154 kb
Candidate markers 260
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 9 remaining regions by MarkerSeek score (out of 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-rps16 LSC 711 0.0559 0.97 83.2 yes View details
trnR-atpA LSC 305 0.0745 0.99 77.8 yes View details
ycf1 IRb 960 0.0025 1.00 49.6 no View details
ndhF-rpl32 SSC 842 0.0474 0.99 83.6 yes View details
rpl32-trnL SSC 765 0.0658 0.98 85.3 yes View details
ycf1 SSC 5166 0.0439 0.98 75.3 yes View details
atpI-rps2 LSC 245 0.0499 1.00 89.2 yes View details
ndhC-trnV LSC 866 0.0420 0.99 86.0 yes View details
trnS-trnG LSC 688 0.0473 0.98 84.9 yes View details
trnG-trnR LSC 142 0.0852 1.00 83.8 yes View details
trnE-trnT LSC 833 0.0333 0.99 83.6 yes View details
rps4-trnT LSC 470 0.0417 0.82 83.4 yes View details
trnD-trnY LSC 414 0.0404 0.99 82.6 yes View details
trnF-ndhJ LSC 683 0.0377 0.89 81.0 yes View details
trnT-trnL LSC 829 0.0277 0.98 80.7 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
trnK-rps16_p1 trnK-rps16 CCTTTCAGGATCAGTCGTGG GAGGTTCGAATCCTTCCGTC 1472–2349 1.000 91.3
trnK-rps16_p2 trnK-rps16 TCAGGATCAGTCGTGGTCTT GAGGTTCGAATCCTTCCGTC 1468–2345 0.938 88.3
trnK-rps16_p3 trnK-rps16 TTCAGGATCAGTCGTGGTCT GAGGTTCGAATCCTTCCGTC 1469–2346 0.938 88.3
trnK-rps16_p4 trnK-rps16 CCTTTCAGGATCAGTCGTGG TCGATCCCGAAGAGAAGGAA 947–1053 0.750 80.8
trnK-rps16_p5 trnK-rps16 CCTTTCAGGATCAGTCGTGG GATTTCCTTAAAACGGGCGC 945–962 0.250 52.4
trnS-trnG_p1 trnS-trnG CCAACGCTTTAGTCCACTCA ACGAATCACACTTTTACCACT 732–816 1.000 62.4
trnS-trnG_p2 trnS-trnG AACGCTTTAGTCCACTCAGC ACGAATCACACTTTTACCACT 730–814 1.000 62.1
trnS-trnG_p3 trnS-trnG CCAACGCTTTAGTCCACTCA AACGAATCACACTTTTACCACT 733–817 1.000 60.5
trnS-trnG_p4 trnS-trnG GCTTTAGTCCACTCAGCCAT ACGAATCACACTTTTACCACT 727–811 1.000 60.4
trnS-trnG_p5 trnS-trnG AACGCTTTAGTCCACTCAGC AACGAATCACACTTTTACCACT 731–815 1.000 60.2
trnG-trnR_p1 trnG-trnR TGATCACTCGACGTCGACTA TGATATTGCGTCCAATAGGA 278–316 0.875 54.4
trnG-trnR_p2 trnG-trnR AGCCTTCCAAGCTAACGATG TGATATTGCGTCCAATAGGA 250–288 0.875 54.2
trnG-trnR_p3 trnG-trnR ACCCTTAGCCTTCCAAGCTA TGATATTGCGTCCAATAGGA 256–294 0.875 54.1
trnG-trnR_p4 trnG-trnR CGACGTCGACTAAAACCCTT TGATATTGCGTCCAATAGGA 270–308 0.875 53.9
trnG-trnR_p5 trnG-trnR AAACCCTTAGCCTTCCAAGC TGATATTGCGTCCAATAGGA 258–296 0.875 53.8
trnR-atpA_p1 trnR-atpA TGATCACTCGACGTCGACTA GGGTCGTGAAGCTTATCCAG 1250–1313 0.938 89.0
trnR-atpA_p2 trnR-atpA TGATCACTCGACGTCGACTA GGTCGTGAAGCTTATCCAGG 1249–1312 0.938 89.0
trnR-atpA_p3 trnR-atpA AGCCTTCCAAGCTAACGATG GGGTCGTGAAGCTTATCCAG 1222–1285 0.938 88.8
trnR-atpA_p4 trnR-atpA AGCCTTCCAAGCTAACGATG GGTCGTGAAGCTTATCCAGG 1221–1284 0.938 88.8
trnR-atpA_p5 trnR-atpA ACCCTTAGCCTTCCAAGCTA GGTCGTGAAGCTTATCCAGG 1227–1290 0.938 88.8
atpI-rps2_p1 atpI-rps2 TGGCCTACTTCTACACCAGA TTCCAGCAAATGATGACGCT 420–446 1.000 83.2
atpI-rps2_p2 atpI-rps2 TGGCCTACTTCTACACCAGA GCAATTTGTGAGGGTCGTTC 361–387 1.000 82.2
atpI-rps2_p3 atpI-rps2 TGGCCTACTTCTACACCAGA TTGTGAGGGTCGTTCTAGCT 356–382 1.000 81.9
atpI-rps2_p4 atpI-rps2 TGGCCTACTTCTACACCAGA TTTGTGAGGGTCGTTCTAGC 357–383 1.000 81.2
atpI-rps2_p5 atpI-rps2 TGGCCTACTTCTACACCAGA TGTGAGGGTCGTTCTAGCTA 355–381 1.000 80.8
trnD-trnY_p1 trnD-trnY CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 480–508 1.000 86.3
trnD-trnY_p2 trnD-trnY CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 479–507 1.000 86.3
trnD-trnY_p3 trnD-trnY CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 501–529 1.000 85.3
trnD-trnY_p4 trnD-trnY CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 500–528 1.000 85.1
trnD-trnY_p5 trnD-trnY CGGTGCTCTGACCAATTGAA GATTCTTCCTGGGTCGATGC 534–562 1.000 84.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (16)

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

Species Accession Length (bp) Link
Heliophila africana MW018451.1 153164 View on NCBI ↗
Heliophila amplexicaulis NC_049643.1 153871 View on NCBI ↗
Heliophila arenaria MW018453.1 154239 View on NCBI ↗
Heliophila biseriata MW018454.1 153892 View on NCBI ↗
Heliophila collina MW018455.1 153952 View on NCBI ↗
Heliophila cornuta MW018456.1 153665 View on NCBI ↗
Heliophila crithmifolia MW018457.1 153935 View on NCBI ↗
Heliophila deserticola MW018458.1 153895 View on NCBI ↗
Heliophila diffusa MW018459.1 153677 View on NCBI ↗
Heliophila elongata MW018460.1 153914 View on NCBI ↗
Heliophila juncea NC_049646.1 153732 View on NCBI ↗
Heliophila lactea MW018462.1 153743 View on NCBI ↗
Heliophila linearis MW018463.1 154039 View on NCBI ↗
Heliophila longifolia NC_049647.1 153931 View on NCBI ↗
Heliophila pusilla NC_049651.1 154136 View on NCBI ↗
Heliophila variabilis MW018465.1 153124 View on NCBI ↗