Markers + reference

Eremogone

5 species · Caryophyllaceae · Caryophyllales

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Species 5
Genome length 134–135 kb
Candidate markers 262
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
petN-psbM LSC 221 0.0201 0.96 70.2 yes View details
trnE-UUC-trnT-GGU LSC 225 0.0498 1.00 89.0 yes View details
trnT-GGU-psbD LSC 507 0.0071 1.00 55.1 yes View details
psbZ-trnG-GCC LSC 284 0.0626 0.99 64.6 yes View details
trnF-GAA-ndhJ LSC 583 0.0134 0.99 62.2 yes View details
petA-psbJ LSC 641 0.0112 1.00 54.3 yes View details
psaJ-rpl33 LSC 379 0.0267 0.98 67.2 yes View details
rpl16 LSC 1157 0.0048 1.00 49.0 yes View details
ycf1 IRb 1809 0.0008 1.00 47.0 no View details
ndhF-rpl32 SSC 408 0.0221 0.98 61.2 yes View details
ycf1 SSC 5433 0.0039 1.00 57.4 yes View details
ndhD-psaC SSC 87 0.0368 1.00 70.2 yes View details
atpF-atpH LSC 372 0.0126 1.00 69.1 yes View details
rpl2-trnH IRa 169 0.0036 1.00 64.4 no View details
psaA-ycf3 LSC 698 0.0059 1.00 64.3 yes View details
atpB-rbcL LSC 727 0.0052 1.00 63.8 yes View details
accD LSC 1413 0.0020 1.00 63.8 yes View details
ndhC-trnV LSC 666 0.0066 1.00 63.3 yes View details
matK-trnK-UUU LSC 655 0.0037 0.99 62.5 yes View details
psbM-trnD-GUC LSC 496 0.0090 0.99 61.6 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_p1 trnK-UUU CCAAAATTCTTTGTCAGTACATGA CGTTGGTTGAATTTGTTCCGA 2652–2685 1.000 41.5
trnK-UUU_p2 trnK-UUU CCAAAATTCTTTGTCAGTACATGA TCGTTGGTTGAATTTGTTCCG 2653–2686 1.000 41.5
trnK-UUU_p3 trnK-UUU CCAAAATTCTTTGTCAGTACATGA AGTCAAGGATTCGTTGGTTGA 2663–2696 1.000 41.5
trnK-UUU_p4 trnK-UUU TCTTTGTCAGTACATGAAGTT CGTTGGTTGAATTTGTTCCGA 2645–2678 1.000 41.5
trnK-UUU_p5 trnK-UUU TCTTTGTCAGTACATGAAGTT TCGTTGGTTGAATTTGTTCCG 2646–2679 1.000 41.5
matK-trnK-UUU_p1 matK-trnK-UUU TGTGTTGACAAGAACTTTCTCG AACGGTAGAGTACTCGGCTT 728–762 1.000 57.9
matK-trnK-UUU_p2 matK-trnK-UUU TGTGTTGACAAGAACTTTCTCG ACGGTAGAGTACTCGGCTTT 727–761 1.000 57.9
matK-trnK-UUU_p3 matK-trnK-UUU GTGTTGACAAGAACTTTCTCGT AACGGTAGAGTACTCGGCTT 727–761 1.000 57.9
matK-trnK-UUU_p4 matK-trnK-UUU GTGTTGACAAGAACTTTCTCGT ACGGTAGAGTACTCGGCTTT 726–760 1.000 57.9
matK-trnK-UUU_p5 matK-trnK-UUU TGTGTTGACAAGAACTTTCTCG AGCTATTACGGGGGTTGCTA 752–786 1.000 57.6
atpF-atpH_p1 atpF-atpH CCAGTGACCCAAGAAAACGA CCGAGGCAGAGGGAAAAATA 531–547 1.000 78.6
atpF-atpH_p2 atpF-atpH TTAACCCCAAAACTCTCGGC CCGAGGCAGAGGGAAAAATA 557–573 1.000 77.9
atpF-atpH_p3 atpF-atpH CCAGTGACCCAAGAAAACGA GCAGAGGGAAAAATACGAGGT 526–542 1.000 76.2
atpF-atpH_p4 atpF-atpH TTAACCCCAAAACTCTCGGC GCAGAGGGAAAAATACGAGGT 552–568 1.000 75.5
atpF-atpH_p5 atpF-atpH CCAGTGACCCAAGAAAACGA TGGTTGTAGCATTAGCCCTT 456–472 1.000 75.5
petN-psbM_p1 petN-psbM ATGGGGAAGAAGTGGACTCT GCTACTGCGCTCTTCATTCT 321–474 1.000 82.6
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT TTGCTACTGCGCTCTTCATT 323–476 1.000 82.3
petN-psbM_p3 petN-psbM ATTCTAAGTCTCGCTTGGGC GCTACTGCGCTCTTCATTCT 383–536 1.000 82.1
petN-psbM_p4 petN-psbM ATTCTAAGTCTCGCTTGGGC TTGCTACTGCGCTCTTCATT 385–538 1.000 81.9
petN-psbM_p5 petN-psbM ATTCTAAGTCTCGCTTGGGC ATTGCTACTGCGCTCTTCAT 386–539 1.000 80.1
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAAGAGCGCAGTAGC TCAATTGGTTAGAGCACCGC 552–615 1.000 80.4
psbM-trnD-GUC_p2 psbM-trnD-GUC AATGAAGAGCGCAGTAGCAA TCAATTGGTTAGAGCACCGC 550–613 1.000 80.1
psbM-trnD-GUC_p3 psbM-trnD-GUC ATGAAGAGCGCAGTAGCAAT TCAATTGGTTAGAGCACCGC 549–612 1.000 78.4
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAATGAAGAGCGCAGTAGC AGCACTTAAGTTGCTTGGGA 633 0.200 42.2
psbM-trnD-GUC_p5 psbM-trnD-GUC AATGAAGAGCGCAGTAGCAA AGCACTTAAGTTGCTTGGGA 631 0.200 42.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 310–588 1.000 86.5
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 312–590 1.000 86.4
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 291–569 1.000 86.1
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 289–567 1.000 86.1
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GATGTCCTGAACCGCTAGAC GAACCGATGACTTACGCCTT 309–587 1.000 85.9

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
Eremogone acicularis NC_069855.1 133638 View on NCBI ↗
Eremogone brevipetala NC_069856.1 133727 View on NCBI ↗
Eremogone bryophylla NC_069857.1 133835 View on NCBI ↗
Eremogone juncea PQ047134.1 134812 View on NCBI ↗
Eremogone kansuensis NC_085476.1 133621 View on NCBI ↗