Markers + reference

Disanthus

2 species · Hamamelidaceae · Saxifragales

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Species 2
Genome length 158–158 kb
Candidate markers 273
Primer pairs 80

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 8 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 310 0.0000 1.00 34.0 yes View details
psbA LSC 1062 0.0000 1.00 40.0 yes View details
rpoC2 LSC 4158 0.0002 1.00 54.0 yes View details
psbC LSC 1422 0.0000 1.00 40.0 yes View details
trnS-UGA-psbZ LSC 348 0.0029 1.00 55.2 yes View details
trnL-UAA-trnF-GAA LSC 361 0.0028 1.00 55.4 yes View details
petA LSC 963 0.0010 1.00 59.3 yes View details
ycf1 SSC 5661 0.0004 1.00 52.7 yes View details
rps16-trnQ-UUG LSC 1434 0.0000 0.99 60.2 yes View details
trnN-GUU-ndhF IRb 1480 0.0000 0.99 59.8 yes View details
matK LSC 1272 0.0008 1.00 59.2 yes View details
trnT-UGU-trnL-UAA LSC 1055 0.0000 1.00 58.8 yes View details
clpP LSC 1959 0.0000 1.00 58.1 yes View details
rps14-psaB LSC 135 0.0000 0.99 53.2 yes View details
rpl2-trnH-GUG IRa 87 0.0000 0.47 45.9 no View details
matK-trnK-UUU LSC 701 0.0000 1.00 40.0 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 80 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 CCTCTAGACCTAGCTGCTGT 376 1.000 78.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 390 1.000 78.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 389 1.000 78.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 391 1.000 78.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 379 1.000 78.4
psbA_p1 psbA TCAAGAGAGTTGGTATTGCTCC TGCTTGGGAGTCCCTGATAA 1164 1.000 62.1
psbA_p2 psbA CAAGAGAGTTGGTATTGCTCCT TGCTTGGGAGTCCCTGATAA 1163 1.000 62.0
psbA_p3 psbA TCAAGAGAGTTGGTATTGCTCC ATGCTTGGGAGTCCCTGATA 1165 1.000 60.8
psbA_p4 psbA TCAAGAGAGTTGGTATTGCTCC TATGCTTGGGAGTCCCTGAT 1166 1.000 60.8
psbA_p5 psbA CAAGAGAGTTGGTATTGCTCCT ATGCTTGGGAGTCCCTGATA 1164 1.000 60.7
trnK-UUU_p1 trnK-UUU TGTGAATGATAGAAGTGAATTACA TCCGACTGTATCTACATACCCT 2659–2660 1.000 40.0
trnK-UUU_p2 trnK-UUU TGTGAATGATAGAAGTGAATTACA TGCATCGTACAATCTGATCTCT 2695–2696 1.000 40.0
trnK-UUU_p3 trnK-UUU TGTGAATGATAGAAGTGAATTACAA TCCGACTGTATCTACATACCCT 2659–2660 1.000 40.0
trnK-UUU_p4 trnK-UUU TTGTGAATGATAGAAGTGAATTACA TCCGACTGTATCTACATACCCT 2660–2661 1.000 40.0
trnK-UUU_p5 trnK-UUU TGTGAATGATAGAAGTGAATTACA TTCCGACTGTATCTACATACCCT 2660–2661 1.000 40.0
matK_p1 matK TCGAGCACAAGAAAGTCGAA CCTTGTTTTGACTGTATCGCA 1380–1381 1.000 58.7
matK_p2 matK TTCGAGCACAAGAAAGTCGA CCTTGTTTTGACTGTATCGCA 1381–1382 1.000 58.7
matK_p3 matK TCGAGCACAAGAAAGTCGAA ACCTTGTTTTGACTGTATCGC 1381–1382 1.000 58.7
matK_p4 matK TTCGAGCACAAGAAAGTCGA ACCTTGTTTTGACTGTATCGC 1382–1383 1.000 58.7
matK_p5 matK TCGAGCACAAGAAAGTCGAA CCTTGTTTTGACTGTATCGCAC 1380–1381 1.000 58.5
matK-trnK-UUU_p1 matK-trnK-UUU GAAGTCAGGTTGCCGAGATT AACGGTAGAGTACTCGGCTT 779 1.000 77.8
matK-trnK-UUU_p2 matK-trnK-UUU GAAGTCAGGTTGCCGAGATT ACGGTAGAGTACTCGGCTTT 778 1.000 77.8
matK-trnK-UUU_p3 matK-trnK-UUU GAAGTCAGGTTGCCGAGATT GGGTTGCTAACTCAACGGTA 792 1.000 75.5
matK-trnK-UUU_p4 matK-trnK-UUU GAAGTCAGGTTGCCGAGATT TTCGGGTTGCTAACTCAACG 795 1.000 75.2
matK-trnK-UUU_p5 matK-trnK-UUU ATAGGAAGTCAGGTTGCCGA ACGGTAGAGTACTCGGCTTT 782 1.000 75.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAGAAACTCGAAATGGGGCG 1547–1568 1.000 79.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1486–1507 1.000 79.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC TAGAAACTCGAAATGGGGCG 1558–1579 1.000 79.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1497–1518 1.000 78.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AAACTCGAAATGGGGCGTAG 1544–1565 1.000 77.8

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
Disanthus cercidifolius NC_084416.1 158116 View on NCBI ↗
Disanthus cercidifolius subsp. longipes NC_050371.1 158076 View on NCBI ↗