Markers + reference

Shivparvatia

2 species · Caryophyllaceae · Caryophyllales

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Species 2
Genome length 138–147 kb
Candidate markers 263
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnS-CGA LSC 746 0.0891 0.74 76.9 yes View details
ndhC LSC 363 0.4068 0.16 64.1 yes View details
clpP LSC 2023 0.0523 0.98 73.7 yes View details
ndhF SSC 2232 0.3605 0.27 69.2 yes View details
rpl32-trnL-UAG SSC 700 0.0974 0.89 84.0 yes View details
ycf3-trnS-GGA LSC 244 0.0972 0.89 81.3 yes View details
atpF-atpH LSC 484 0.0729 0.91 80.5 yes View details
trnK-UUU-rps16 LSC 637 0.0772 0.96 80.3 yes View details
rps16-trnQ-UUG LSC 685 0.0708 0.89 79.8 yes View details
trnR-UCU-atpA LSC 98 0.1020 1.00 77.5 yes View details
trnL-UAG-ccsA SSC 139 0.0853 0.93 77.4 yes View details
rpl16 LSC 1352 0.0541 0.97 77.1 yes View details
rps4-trnT-UGU LSC 178 0.0710 0.95 77.0 yes View details
petA-psbJ LSC 854 0.0617 0.85 77.0 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-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA AAAGAGGGCGGCAGTTTTTA 774 0.500 59.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA AAGAGGGCGGCAGTTTTTAA 773 0.500 59.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA AGAGGGCGGCAGTTTTTAAA 772 0.500 59.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA AGGGCGGCAGTTTTTAAAGA 770 0.500 59.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA TAAAGAGGGCGGCAGTTTTT 775 0.500 59.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCACAACGGATCATGTCCTT TTCGGAGGTTCGAATCCTTC 722–783 1.000 82.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 701–762 1.000 82.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC TTCGGAGGTTCGAATCCTTC 712–773 1.000 81.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TGTCGAGTCAAGAGCATCCT TTCGGAGGTTCGAATCCTTC 768–829 1.000 79.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATGTCGAGTCAAGAGCATCC TTCGGAGGTTCGAATCCTTC 769–830 1.000 78.2
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA CTTTCGTCCACTCAGCCATC ACCACTAAACTATACCCGCT 614–791 1.000 65.7
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA TTTCGTCCACTCAGCCATCT ACCACTAAACTATACCCGCT 613–790 1.000 62.6
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA TCCACTCAGCCATCTCTCC ACCACTAAACTATACCCGCT 608–785 1.000 62.1
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA GATTAGCAATCCGACGCTTTC ACCACTAAACTATACCCGCT 630–807 1.000 60.7
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA TTCGTCCACTCAGCCATCT ACCACTAAACTATACCCGCT 612–789 1.000 60.1
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCAAGAACAGATGGAACGCT 163–210 1.000 64.0
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TGGAACGCTTTCTACTTCAGG 152–199 1.000 62.7
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCAAGAACAGATGGAACGCTT 163–210 1.000 61.7
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCAAGAACAGATGGAACGCT 164–211 1.000 61.7
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT TCAAGAACAGATGGAACGCT 198–245 1.000 60.5
atpF-atpH_p1 atpF-atpH CCAGTGACCCAAGAAAACGA CCGAGGGAAAAATACGAGGT 604–639 1.000 82.3
atpF-atpH_p2 atpF-atpH CCAGTGACCCAAGAAAACGA GCCGAGGGAAAAATACGAGG 605–640 1.000 82.2
atpF-atpH_p3 atpF-atpH CCAGTGACCCAAGAAAACGA TGGTTGTAGCATTAGCCCTT 535–570 1.000 78.8
atpF-atpH_p4 atpF-atpH CCAGTGACCCAAGAAAACGA TTGGTTGTAGCATTAGCCCT 536–571 1.000 78.8
atpF-atpH_p5 atpF-atpH CCAGTGACCCAAGAAAACGA TGGTTGTAGCATTAGCCCTTT 535–570 1.000 76.7
ycf3-trnS-GGA_p1 ycf3-trnS-GGA TGCCTCTTTTTCTCCCGAAG TTCCAATGCTACGCCTTGAA 368–387 1.000 85.4
ycf3-trnS-GGA_p2 ycf3-trnS-GGA GCCTCTTTTTCTCCCGAAGT TTCCAATGCTACGCCTTGAA 367–386 1.000 85.4
ycf3-trnS-GGA_p3 ycf3-trnS-GGA TGCCTCTTTTTCTCCCGAAG ACGGAAAGAGAGGGATTCGA 418–437 1.000 85.2
ycf3-trnS-GGA_p4 ycf3-trnS-GGA GCCTCTTTTTCTCCCGAAGT ACGGAAAGAGAGGGATTCGA 417–436 1.000 85.2
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TGCCTCTTTTTCTCCCGAAG AGTTCCAATGCTACGCCTTG 370–389 1.000 82.6

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
Shivparvatia glanduligera NC_069858.1 146977 View on NCBI ↗
Shivparvatia melandryiformis PV640849.1 137506 View on NCBI ↗