Markers + reference

Acanthophyllum

2 species · Caryophyllaceae · Caryophyllales

Back to catalogue

Species 2
Genome length 150–151 kb
Candidate markers 260
Primer pairs 105

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 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0009 1.00 44.9 yes View details
trnS-GCU-trnG-UCC LSC 740 0.0081 1.00 63.7 yes View details
rpoC1 LSC 2806 0.0047 0.99 59.2 yes View details
trnE-UUC-trnT-GGU LSC 588 0.0172 0.99 69.2 yes View details
psbE-petL LSC 1276 0.0078 1.00 63.3 yes View details
psaJ-rpl33 LSC 455 0.0132 1.00 63.7 yes View details
petD LSC 1250 0.0066 0.98 51.0 yes View details
rpl16 LSC 1310 0.0062 0.99 50.5 yes View details
rpl32-trnL-UAG SSC 960 0.0115 1.00 65.4 yes View details
ycf1 SSC 5613 0.0036 1.00 43.4 yes View details
atpA-atpF LSC 60 0.0333 1.00 71.7 yes View details
rbcL-accD LSC 746 0.0028 0.97 63.1 yes View details
petN-psbM LSC 1091 0.0073 1.00 62.9 yes View details
trnR-ACG-trnN-GUU IRb 587 0.0068 1.00 62.4 yes View details
trnN-GUU-trnR-ACG IRa 587 0.0068 1.00 62.4 yes View details
trnR-UCU-atpA LSC 121 0.0168 0.98 62.1 yes View details
atpF-atpH LSC 476 0.0044 0.96 62.1 yes View details
psaA-ycf3 LSC 1084 0.0055 1.00 62.1 yes View details
trnT-GGU-psbD LSC 840 0.0048 1.00 61.7 yes View details
ycf4-cemA LSC 772 0.0052 1.00 61.7 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA CTACATCCGCCCTTTTGTGT TTGACACGGGCATATAAGGC 1386–1387 1.000 78.7
psbA_p2 psbA TACATCCGCCCTTTTGTGTC TTGACACGGGCATATAAGGC 1385–1386 1.000 78.7
psbA_p3 psbA CTACATCCGCCCTTTTGTGT TGGGGAGGGGTTTTTCCTAT 1591–1595 1.000 78.3
psbA_p4 psbA TACATCCGCCCTTTTGTGTC TGGGGAGGGGTTTTTCCTAT 1590–1594 1.000 78.3
psbA_p5 psbA TCACAATCCACTGCCTTGAG TTGACACGGGCATATAAGGC 1415 0.500 58.2
trnK-UUU_p1 trnK-UUU TGAGACGCACCTGAATTCTT TCGTAACAGGAATCAACTCGA 2726–2727 1.000 56.2
trnK-UUU_p2 trnK-UUU TTGAGACGCACCTGAATTCT TCGTAACAGGAATCAACTCGA 2727–2728 1.000 56.2
trnK-UUU_p3 trnK-UUU ACGCACCTGAATTCTTTGTG TCGTAACAGGAATCAACTCGA 2722–2723 1.000 54.4
trnK-UUU_p4 trnK-UUU GACGCACCTGAATTCTTTGTG TCGTAACAGGAATCAACTCGA 2723–2724 1.000 54.2
trnK-UUU_p5 trnK-UUU TGAGACGCACCTGAATTCTTT TCGTAACAGGAATCAACTCGA 2726–2727 1.000 53.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG TCAAACCGAGAGACCCCTTA 905 1.000 77.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG AACCGAGAGACCCCTTAACT 902 1.000 77.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG AATCAAACCGAGAGACCCCT 907 1.000 77.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG ATCAAACCGAGAGACCCCTT 906 1.000 77.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TCAAACCGAGAGACCCCTTA 904 1.000 77.0
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TGGAACGCTTTCTACTTCAGG 176 1.000 60.0
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GGAACGCTTTCTACTTCAGGA 175 1.000 57.8
trnR-UCU-atpA_p3 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT TGGAACGCTTTCTACTTCAGG 211 1.000 56.8
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACATTTACTGAGGAAGCGGA 228 1.000 56.3
trnR-UCU-atpA_p5 trnR-UCU-atpA GGAATGAAATGAAAAGCGTCCA TGGAACGCTTTCTACTTCAGG 241 1.000 55.6
atpA-atpF_p1 atpA-atpF TTTCGTCTGCTCGAATGGTT AATATTGGCATGTTTGGGGC 127 1.000 71.9
atpA-atpF_p2 atpA-atpF TCGTCTGCTCGAATGGTTAC AATATTGGCATGTTTGGGGC 125 1.000 71.0
atpA-atpF_p3 atpA-atpF ACTTGGAGTACGGTACCAGT AATATTGGCATGTTTGGGGC 206 1.000 70.3
atpA-atpF_p4 atpA-atpF GTCTGCTCGAATGGTTACCA AATATTGGCATGTTTGGGGC 123 1.000 70.2
atpA-atpF_p5 atpA-atpF ATTTCGTCTGCTCGAATGGT AATATTGGCATGTTTGGGGC 128 1.000 70.1
atpF-atpH_p1 atpF-atpH AGTGACCCAAGAAAGCGAAA GATTGGTTGTCGCATTAGCC 546–563 1.000 76.2
atpF-atpH_p2 atpF-atpH AGTGACCCAAGAAAGCGAAA GGATTGGTTGTCGCATTAGC 547–564 1.000 76.2
atpF-atpH_p3 atpF-atpH CAGTGACCCAAGAAAGCGAA GATTGGTTGTCGCATTAGCC 547–564 1.000 75.7
atpF-atpH_p4 atpF-atpH CAGTGACCCAAGAAAGCGAA GGATTGGTTGTCGCATTAGC 548–565 1.000 75.7
atpF-atpH_p5 atpF-atpH AGTGACCCAAGAAAGCGAAA CCTGAGGCAGAGGGAAAAAT 619–636 1.000 75.5

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
Acanthophyllum aculeatum PZ094841.1 150911 View on NCBI ↗
Acanthophyllum pungens NC_087605.1 150491 View on NCBI ↗