Markers + reference

Drymaria

2 species · Caryophyllaceae · Caryophyllales

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Species 2
Genome length 151–151 kb
Candidate markers 260
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 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
rpoB-trnC-GCA LSC 757 0.1028 0.99 80.0 yes View details
psaA-ycf3 LSC 1075 0.0943 0.89 82.4 yes View details
trnT-UGU-trnL-UAA LSC 818 0.1285 0.92 84.0 yes View details
ndhC-trnV-UAC LSC 1040 0.1033 0.94 85.1 yes View details
petA-psbJ LSC 973 0.1045 0.81 78.1 yes View details
psbE-petL LSC 972 0.0922 0.96 85.8 yes View details
rpl32-trnL-UAG SSC 971 0.1372 0.68 75.5 yes View details
ycf1 SSC 5574 0.0716 0.98 70.5 yes View details
trnI-GAU-trnA-UGC IRb 70 0.1429 1.00 86.8 yes View details
trnA-UGC-trnI-GAU IRa 70 0.1429 1.00 86.8 yes View details
rps16-trnQ-UUG LSC 635 0.1061 0.95 83.8 yes View details
trnW-CCA-trnP-UGG LSC 166 0.0897 0.94 83.5 yes View details
matK-trnK-UUU LSC 733 0.0767 0.96 82.8 yes View details
trnS-GCU-trnG-UCC LSC 548 0.1014 0.92 82.7 yes View details
rpl36-rps8 LSC 445 0.1253 0.91 81.8 yes View details
petN-psbM LSC 582 0.0879 0.98 81.0 yes View details
trnF-GAA-ndhJ LSC 502 0.0832 0.98 80.7 yes View details
trnH-GUG-psbA LSC 253 0.1392 0.94 80.3 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTAGCTGCTATCGAAGTTCC 311–330 1.000 82.8
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTAGCTGCTATCGAAGTTCC 325–344 1.000 82.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTAGCTGCTATCGAAGTTCC 324–343 1.000 82.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTAGCTGCTATCGAAGTTCC 326–345 1.000 82.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG AGACCTAGCTGCTATCGAAGT 314–333 1.000 82.4
matK-trnK-UUU_p1 matK-trnK-UUU TGTTGCCAAGATCTTTCTAGTTCT AACGGTAGAGTACTCGGCTT 785–804 1.000 54.0
matK-trnK-UUU_p2 matK-trnK-UUU TGTTGCCAAGATCTTTCTAGTTCT ACGGTAGAGTACTCGGCTTT 784–803 1.000 54.0
matK-trnK-UUU_p3 matK-trnK-UUU TGTTGCCAAGATCTTTCTAGT AACGGTAGAGTACTCGGCTT 785–804 1.000 53.8
matK-trnK-UUU_p4 matK-trnK-UUU TGTTGCCAAGATCTTTCTAGT ACGGTAGAGTACTCGGCTTT 784–803 1.000 53.8
matK-trnK-UUU_p5 matK-trnK-UUU TGTTGCCAAGATCTTTCTAGTTC ACGGTAGAGTACTCGGCTTT 784–803 1.000 53.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GCGAAGAAACAGCTACTCGA 1161–1164 1.000 89.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCGGATCATGTCCTTCAAGT GCGAAGAAACAGCTACTCGA 1159–1162 1.000 89.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA AACCAAGTAATGCGGGTTGT 1439 0.500 59.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GCGGATCATGTCCTTCAAGT AACCAAGTAATGCGGGTTGT 1437 0.500 59.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCAACAAGAAATGCGGGTTC AACCAAGTAATGCGGGTTGT 1533 0.500 59.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TACCACTAAACTATACCCGC 619–657 1.000 57.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TTACCACTAAACTATACCCGC 620–658 1.000 56.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TTTACCACTAAACTATACCCGC 621–659 1.000 54.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC TACCACTAAACTATACCCGC 555–593 1.000 53.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AACGGAAAGAGAGGGATTCG TACCACTAAACTATACCCGC 620–658 1.000 52.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CCATTCTTGACCTGCGGTTA 1749–1858 1.000 85.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CCGGATTTGAACTGGGGAAA 1332–1424 1.000 85.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCGGGGCTTTGCAATATTTG CCGGATTTGAACTGGGGAAA 1212–1304 1.000 85.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CTCCCTGTCGGTTTTCCAAA CCGGATTTGAACTGGGGAAA 1099 0.500 59.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CTCCCTGTCGGTTTTCCAAA CCATTCTTGACCTGCGGTTA 1516 0.500 58.9
petN-psbM_p1 petN-psbM AGTATGGGGAAGAAGTGGACT AAAACGGTCAGCCAAAATGA 631–661 1.000 65.7
petN-psbM_p2 petN-psbM AGTATGGGGAAGAAGTGGACT AAACGGTCAGCCAAAATGAT 630–660 1.000 63.9
petN-psbM_p3 petN-psbM AGTATGGGGAAGAAGTGGACT AACGGTCAGCCAAAATGATT 629–659 1.000 63.9
petN-psbM_p4 petN-psbM AGTATGGGGAAGAAGTGGACT AAAAACGGTCAGCCAAAATGA 632–662 1.000 63.7
petN-psbM_p5 petN-psbM AGTATGGGGAAGAAGTGGACT TGTAAAAACGGTCAGCCAAA 635–665 1.000 62.8

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
Drymaria cordata NC_087606.1 151288 View on NCBI ↗
Drymaria villosa OR790517.1 150750 View on NCBI ↗