Markers + reference

Dialium

3 species · Fabaceae · Fabales

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Species 3
Genome length 159–162 kb
Candidate markers 268
Primer pairs 100

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 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 577 0.0300 1.00 59.4 yes View details
trnQ-UUG-psbK LSC 530 0.0302 1.00 53.0 yes View details
trnS-GCU-trnG-UCC LSC 700 0.0248 1.00 71.2 yes View details
trnR-UCU-atpA LSC 713 0.0374 1.00 64.1 yes View details
atpH-atpI LSC 967 0.0290 1.00 51.6 yes View details
psbZ-trnG-GCC LSC 556 0.0300 1.00 60.6 yes View details
ndhC-trnV-UAC LSC 673 0.0594 1.00 83.5 yes View details
rbcL-accD LSC 949 0.0183 1.00 44.9 yes View details
accD-psaI LSC 590 0.0463 1.00 64.4 yes View details
trnP-UGG-psaJ LSC 589 0.0385 1.00 63.7 yes View details
rpl32-trnL-UAG SSC 1123 0.0208 1.00 71.6 yes View details
trnW-CCA-trnP-UGG LSC 181 0.0479 1.00 66.6 yes View details
psbF-psbE LSC 9 0.0741 1.00 66.2 yes View details
trnH-GUG-psbA LSC 317 0.0315 1.00 66.0 yes View details
trnG-GCC-trnfM-CAU LSC 279 0.0311 1.00 64.5 yes View details
trnK-UUU-rps16 LSC 693 0.0250 1.00 64.2 yes View details
rpl33-rps18 LSC 344 0.0407 1.00 61.6 yes View details
ycf1-ndhF SSC 5 0.2667 1.00 60.9 yes View details
trnT-UGU-trnL-UAA LSC 1118 0.0095 1.00 57.8 yes View details
petN-psbM LSC 1295 0.0082 1.00 53.3 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 100 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 GCGCTAACCTTGGTATGGAA 429–433 1.000 85.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 443–447 1.000 85.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 442–446 1.000 85.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 444–448 1.000 85.3
trnH-GUG-psbA_p5 trnH-GUG-psbA CAAATTATGGGCGAACGACG GCGCTAACCTTGGTATGGAA 491–495 1.000 85.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GCGGGTGTTTCTATGGAACT 789–1352 1.000 77.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 GAGTCGCACTTAAAAGCCGA GCGGGTGTTTCTATGGAACT 790–1353 1.000 77.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGAGTCGCACTTAAAAGCC GCGGGTGTTTCTATGGAACT 792–1355 1.000 77.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG AAAGGGCGGGTGTTTCTATG 794–1357 1.000 77.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 GAGTCGCACTTAAAAGCCGA AAAGGGCGGGTGTTTCTATG 795–1358 1.000 77.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 645–671 1.000 85.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AGTCGCACGTTGCTTTTTAC GAGGTTCGAATCCTTCCGTC 649–675 1.000 83.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAAGTCGCACGTTGCTTTTT GAGGTTCGAATCCTTCCGTC 651–677 1.000 82.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GTCGCACGTTGCTTTTTACC GAGGTTCGAATCCTTCCGTC 648–674 1.000 81.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA TTCGGAGGTTCGAATCCTTC 649–675 1.000 80.3
trnQ-UUG-psbK_p1 trnQ-UUG-psbK ATCATGCCTTTCAAGTCGCA CTTCAGGCAATTTCGCGAAG 1325–1431 1.000 84.1
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GATCTTCCAAGTGACGCGAT CTTCAGGCAATTTCGCGAAG 850–934 1.000 82.3
trnQ-UUG-psbK_p3 trnQ-UUG-psbK TGGATATGTTCTGGGACGGA CTTCAGGCAATTTCGCGAAG 697–777 1.000 82.1
trnQ-UUG-psbK_p4 trnQ-UUG-psbK TCTTCCAAGTGACGCGATTT CTTCAGGCAATTTCGCGAAG 848–932 1.000 81.5
trnQ-UUG-psbK_p5 trnQ-UUG-psbK GATCTTCCAAGTGACGCGAT TTACGTCCTGGGTCGTTAGA 1423–1523 1.000 80.6
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGAATCAAACGAAGGACCCC 812–1003 1.000 81.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGAATCAAACGAAGGACCCC 811–1002 1.000 81.2
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TGGACGGAAAGAGAGGGATT TGAATCAAACGAAGGACCCC 869–1060 1.000 80.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGGGCCAATAGAACGAATCA 781–972 1.000 80.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TGAATCAAACGAAGGACCCC 866–1057 1.000 79.9
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCAGGAACAGATGGAACTCT 787–891 1.000 54.1
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCAGGAACAGATGGAACTCTT 787–891 1.000 52.6
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCAGGAACAGATGGAACTCT 788–892 1.000 52.6
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGCTATTCAGGAACAGATGGA 793–897 1.000 51.4
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCAGGAACAGATGGAACTCTTT 787–891 1.000 50.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Dialium guianense PV870823.1 159171 View on NCBI ↗
Dialium guineense MW628968.1 161716 View on NCBI ↗
Dialium schlechteri NC_047326.1 159190 View on NCBI ↗