Markers + reference

Dillenia

2 species · Dilleniaceae · Dilleniales

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Species 2
Genome length 159–163 kb
Candidate markers 273
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 9 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 346 0.0301 0.77 61.5 yes View details
trnK-UUU-rps16 LSC 748 0.0179 0.82 66.1 yes View details
trnS-GCU-trnG-GCC LSC 1047 0.1277 0.79 94.0 yes View details
psbM-trnD-GUC LSC 1129 0.0134 0.73 55.0 yes View details
trnT-GGU-psbD LSC 1246 0.0289 1.00 75.4 yes View details
ndhC-trnV-UAC LSC 718 0.1585 0.99 94.4 yes View details
psaJ-rpl33 LSC 351 0.0399 1.00 76.5 yes View details
rpl32-trnL-UAG SSC 972 0.0669 1.00 75.6 yes View details
trnR-ACG-trnN-GUU IRb 606 0.0086 0.96 68.0 yes View details
trnN-GUU-trnR-ACG IRa 606 0.0086 0.96 68.0 yes View details
trnF-GAA-ndhJ LSC 702 0.0157 1.00 67.8 yes View details
rps16-trnQ-UUG LSC 978 0.0043 0.95 65.9 yes View details
rpl16 LSC 1489 0.0042 0.97 64.4 yes View details
ycf15-trnL-CAA IRb 628 0.0096 1.00 64.2 yes View details
trnL-CAA-ycf15 IRa 628 0.0096 1.00 64.2 yes View details
rpoB-trnC-GCA LSC 1111 0.0028 0.96 64.1 yes View details
petA-psbJ LSC 1117 0.0040 0.89 64.1 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 CCTCTAGACCTAGCTGCTGT 334–413 1.000 84.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 348–427 1.000 84.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 347–426 1.000 84.1
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 337–416 1.000 84.1
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 349–428 1.000 84.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AAGGAGCTTCGCCTTAATGA 882–919 1.000 75.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AGGAGCTTCGCCTTAATGAA 881–918 1.000 75.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AGTTTTTAAGGAGCTTCGCCT 889–926 1.000 75.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAGGAGCTTCGCCTTAATGA 830–867 1.000 74.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AGGAGCTTCGCCTTAATGAA 829–866 1.000 74.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCCAATGGTGGGCGTAAAAA GAGGTTCGAATCCTTCCGTC 1093–1658 1.000 82.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTCCAATGGTGGGCGTAAAA GAGGTTCGAATCCTTCCGTC 1094–1659 1.000 82.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCCAATGGTGGGCGTAAAAA AGAAATCTCAATGGGGCGTG 1152–1717 1.000 80.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TTCCAATGGTGGGCGTAAAA AGAAATCTCAATGGGGCGTG 1153–1718 1.000 80.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATGGTGGGCGTAAAAATCCA GAGGTTCGAATCCTTCCGTC 1089–1654 1.000 80.6
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CCGACGCTTTAATCCACTCA ACGAATCGCACTTTTACCACT 935–1112 1.000 82.1
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC CCGACGCTTTAATCCACTCA ACGAATCGCACTTTTACCAC 935–1112 1.000 82.0
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA ACGAATCGCACTTTTACCACT 993–1170 1.000 80.7
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA ACGAATCGCACTTTTACCAC 993–1170 1.000 80.6
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ACGAAAACGGAAAGAGAGGG ACGAATCGCACTTTTACCACT 999–1176 1.000 80.5
trnG-GCC_p1 trnG-GCC CCGATTCCCTTGTTCGACAA TCAGAGTCAATTCAATGATGA 945–965 1.000 41.9
trnG-GCC_p2 trnG-GCC TTGTCCGATTCCCTTGTTCG TCAGAGTCAATTCAATGATGA 949–969 1.000 41.9
trnG-GCC_p3 trnG-GCC GCCCCTGCCTGAAAGATATC TCAGAGTCAATTCAATGATGA 1004–1024 1.000 41.8
trnG-GCC_p4 trnG-GCC GCCCCTGCCTGAAAGATATC ATCAGAGTCAATTCAATGATGA 1025 0.500 20.0
trnG-GCC_p5 trnG-GCC CCGATTCCCTTGTTCGACAA ATCAGAGTCAATTCAATGATGA 966 0.500 20.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCTTCTGCCAAGCCTTGATC CCGGATTTGAACTGGGGAAA 1274–1392 1.000 81.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TACCTCATTTCCATCCCCGA CCGGATTTGAACTGGGGAAA 1197–1315 1.000 80.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CTTCTGCCAAGCCTTGATCA CCGGATTTGAACTGGGGAAA 1273–1391 1.000 80.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TGCCAAGCCTTGATCAATGA CCGGATTTGAACTGGGGAAA 1269–1387 1.000 80.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TTCTGCCAAGCCTTGATCAA CCGGATTTGAACTGGGGAAA 1272–1390 1.000 79.8

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
Dillenia indica NC_042740.1 159266 View on NCBI ↗
Dillenia turbinata NC_062798.1 163250 View on NCBI ↗