Markers + reference

Paronychia

2 species · Caryophyllaceae · Caryophyllales

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Species 2
Genome length 151–151 kb
Candidate markers 266
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 569 0.0935 0.94 82.9 yes View details
psbM-trnD-GUC LSC 648 0.0844 0.93 86.0 yes View details
trnT-GGU-psbD LSC 934 0.0696 0.94 79.6 yes View details
trnT-UGU-trnL-UAA LSC 663 0.0736 0.96 81.8 yes View details
rpl33-rps18 LSC 293 0.1263 0.97 77.5 yes View details
ycf1 IRb 1857 0.0178 1.00 53.7 no View details
ndhF SSC 2238 0.0493 1.00 71.2 yes View details
ndhF-rpl32 SSC 613 0.0881 0.91 82.7 yes View details
rpl32-trnL-UAG SSC 658 0.1155 0.96 86.8 yes View details
ycf1 SSC 5643 0.0552 1.00 67.5 yes View details
rps16-trnQ-UUG LSC 684 0.0776 0.96 86.2 yes View details
trnG-GCC-trnfM-CAU LSC 204 0.1082 0.95 83.0 yes View details
trnF-GAA-ndhJ LSC 408 0.0825 0.98 81.8 yes View details
atpH-atpI LSC 758 0.0499 0.95 80.7 yes View details
trnD-GUC-trnY-GUA LSC 282 0.0849 0.96 80.0 yes View details
psbE-petL LSC 1127 0.0576 0.96 80.0 yes View details
ndhC-trnV-UAC LSC 876 0.0482 0.95 79.9 yes View details
psaA-pafI LSC 777 0.0728 0.92 79.7 yes View details
trnI-CAU-rpl23 IRa 165 0.1234 0.93 79.6 yes View details
trnE-UUC-trnT-GGU LSC 440 0.0837 0.92 79.5 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCACAACGGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 778–807 1.000 86.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 757–786 1.000 86.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 768–797 1.000 85.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAACGGATCATGTCCTT TAAGGCATCGGGTTTTGGTC 808–837 1.000 85.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCATCGGGTTTTGGTC 787–816 1.000 85.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC ACGAATCACACTTTTACCACT 622–949 1.000 51.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC AGAACGAATCACACTTTTACCAC 625–952 1.000 50.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC GAACGAATCACACTTTTACCACT 624–951 1.000 50.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC AGGGGTTAATAGAACGAATCACA 635–962 1.000 50.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC GGGGTTAATAGAACGAATCACAC 634–961 1.000 49.8
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCCGCAG 829–845 1.000 85.5
atpH-atpI_p2 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCCGCAG 830–846 1.000 84.3
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT ACCTGTCATGTTCCTGGGAT 877–893 1.000 83.6
atpH-atpI_p4 atpH-atpI TCCAGCAGCAATAACGGAAG TTTTGCAACTTTAGCCGCAG 839–855 1.000 83.6
atpH-atpI_p5 atpH-atpI ATAACGGAAGCGGCAGAAAT TACCTGTCATGTTCCTGGGA 878–894 1.000 83.5
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAAGAGTGCAGTAGC TCAATTGGTTAGAGCACCGC 743–758 1.000 62.5
psbM-trnD-GUC_p2 psbM-trnD-GUC ACTAGAATGAAGAGTGCAGTAGC TCAATTGGTTAGAGCACCGC 746–761 1.000 61.0
psbM-trnD-GUC_p3 psbM-trnD-GUC AGGAACTAGAATGAAGAGTGCAG TCAATTGGTTAGAGCACCGC 750–765 1.000 60.3
psbM-trnD-GUC_p4 psbM-trnD-GUC AGGAACTAGAATGAAGAGTGCA TCAATTGGTTAGAGCACCGC 750–765 1.000 59.6
psbM-trnD-GUC_p5 psbM-trnD-GUC GGAACTAGAATGAAGAGTGCAGT TCAATTGGTTAGAGCACCGC 749–764 1.000 59.6
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA TGGCAATATGTCTACGCTGG 353–403 1.000 80.9
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA GGCAATATGTCTACGCTGGT 352–402 1.000 80.9
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA GGGGACGGACTGTAAATTCG 374–424 1.000 79.6
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA GGGACGGACTGTAAATTCGT 373–423 1.000 79.4
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA GATTCTTCCTGGGTCGATGC 407–457 1.000 78.6
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 522–550 1.000 86.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 501–529 1.000 86.5
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA TGGCGTTACTCTACCACTGA 498–526 1.000 86.4
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCGATGACTTACGCCTTACC 519–547 1.000 85.6
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA TTGAACCGATGACTTACGCC 524–552 1.000 84.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Paronychia argentea NC_066008.1 150634 View on NCBI ↗
Paronychia canadensis NC_087612.1 151475 View on NCBI ↗