Markers + reference

Periandra

2 species · Fabaceae · Fabales

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Species 2
Genome length 153–154 kb
Candidate markers 265
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 12 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnL-UAA-trnT-UGU LSC 1053 0.0258 0.96 72.0 yes View details
trnG-UCC-trnS-GCU LSC 829 0.0311 0.97 67.4 yes View details
psaJ-rpl33 LSC 501 0.0370 0.97 76.0 yes View details
rps8-rpl14 LSC 410 0.0521 0.98 73.5 yes View details
rpl16 LSC 1588 0.0221 1.00 57.9 yes View details
ycf1 IRb 461 0.0065 1.00 45.6 no View details
ndhF SSC 2244 0.0169 1.00 52.6 yes View details
ndhF-rpl32 SSC 710 0.0272 0.98 62.0 yes View details
rpl32-trnL-CAA SSC 527 0.0368 0.93 67.5 yes View details
ndhA SSC 2322 0.0190 0.99 61.9 yes View details
rps15-ycf1 SSC 397 0.0349 0.94 64.7 yes View details
ycf1 SSC 5412 0.0174 1.00 48.7 yes View details
trnL-CAA-ccsA SSC 92 0.0930 0.93 75.6 yes View details
trnL-CAA SSC 81 0.3165 0.98 74.9 yes View details
psbD-trnT-GGU LSC 1409 0.0193 0.99 70.7 yes View details
ndhE-ndhG SSC 256 0.0480 0.98 70.0 yes View details
trnG-GCC-psbZ LSC 350 0.0261 0.99 69.9 yes View details
rps16-accD LSC 641 0.0159 0.88 69.2 yes View details
ndhJ-trnF-GAA LSC 611 0.0196 1.00 68.5 yes View details
atpA-trnR-UCU LSC 396 0.0319 0.95 68.1 yes View details
trnK-UUU-rbcL LSC 666 0.0140 0.97 66.8 yes View details
trnT-UGU-rps4 LSC 281 0.0360 0.99 66.7 yes View details
trnL-CAA IRb 81 0.0000 1.00 33.8 no View details
trnL-CAA IRa 81 0.0000 1.00 33.8 no 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
trnK-UUU-rbcL_p1 trnK-UUU-rbcL TGGACGAACCAATTGCTTCA AGTCCTGAATTAGCTGCTGC 821–825 1.000 83.1
trnK-UUU-rbcL_p2 trnK-UUU-rbcL TGGACGAACCAATTGCTTCA GAGGCTAGCAAATGGAGTCC 836–840 1.000 83.0
trnK-UUU-rbcL_p3 trnK-UUU-rbcL TGGACGAACCAATTGCTTCA GCTGCTTGTGAGGTATGGAA 806–810 1.000 82.5
trnK-UUU-rbcL_p4 trnK-UUU-rbcL TGGACGAACCAATTGCTTCA GGCTAGCAAATGGAGTCCTG 834–838 1.000 80.7
trnK-UUU-rbcL_p5 trnK-UUU-rbcL TGGACGAACCAATTGCTTCA GTGAGGCTAGCAAATGGAGT 838–842 1.000 80.0
ndhJ-trnF-GAA_p1 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC GGGATAGCTCAGCTGGTAGA 751–779 1.000 80.7
ndhJ-trnF-GAA_p2 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC GCTTCAAGAATGGTCGGGAT 766–794 1.000 80.3
ndhJ-trnF-GAA_p3 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC CCTCGTGTCACCAGTTCAAA 715–743 1.000 80.3
ndhJ-trnF-GAA_p4 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC AGAATGGTCGGGATAGCTCA 760–788 1.000 80.0
ndhJ-trnF-GAA_p5 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC CTGGTAGAGCAGAGGACTGA 739–767 1.000 79.6
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GCGATGCTCTAACCTCTGAG 1078–1103 1.000 84.1
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC AAAGCCAGCTATCGGAATCG 1123–1148 1.000 83.9
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 1086–1111 1.000 83.6
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC AAAGCCAGCTATCGGAATCG 1131–1156 1.000 83.4
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC TCGAGAAAAGCCAGCTATCG 1129–1154 1.000 83.3
trnT-UGU-rps4_p1 trnT-UGU-rps4 CTCAGAGGTTAGAGCATCGC AGGTCCTCTGTAACGTGACA 362–365 1.000 81.7
trnT-UGU-rps4_p2 trnT-UGU-rps4 GGTTCGATTCCGATAGCTGG AGGTCCTCTGTAACGTGACA 321–324 1.000 81.4
trnT-UGU-rps4_p3 trnT-UGU-rps4 CTCAGAGGTTAGAGCATCGC TCGCTTTTTACTGTTGGCCT 433–436 1.000 81.1
trnT-UGU-rps4_p4 trnT-UGU-rps4 ATGGTCATCGGTTCGATTCC AGGTCCTCTGTAACGTGACA 330–333 1.000 81.1
trnT-UGU-rps4_p5 trnT-UGU-rps4 GGTTCGATTCCGATAGCTGG TCGCTTTTTACTGTTGGCCT 392–395 1.000 80.7
trnG-GCC-psbZ_p1 trnG-GCC-psbZ AAATTAAGTAGGCAGGGGCG CTTCTCCTGATGGTTGGTCG 542–544 1.000 81.5
trnG-GCC-psbZ_p2 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA CTTCTCCTGATGGTTGGTCG 502–504 1.000 80.7
trnG-GCC-psbZ_p3 trnG-GCC-psbZ AAATTAAGTAGGCAGGGGCG TTGCTTCTCCTGATGGTTGG 545–547 1.000 80.0
trnG-GCC-psbZ_p4 trnG-GCC-psbZ AAATTAAGTAGGCAGGGGCG TCCTGATGGTTGGTCGAGTA 538–540 1.000 79.9
trnG-GCC-psbZ_p5 trnG-GCC-psbZ AAATTAAGTAGGCAGGGGCG GCTTCTCCTGATGGTTGGTC 543–545 1.000 79.6
psbD-trnT-GGU_p1 psbD-trnT-GGU AAGCAATAGACCGGACCAAC GTGGTAGAGTAACGCCATGG 1580–1581 1.000 80.6
psbD-trnT-GGU_p2 psbD-trnT-GGU AAGCAATAGACCGGACCAAC TCAGTGGTAGAGTAACGCCA 1583–1584 1.000 80.5
psbD-trnT-GGU_p3 psbD-trnT-GGU CACAAAAACGAAACGGTCCC GTGGTAGAGTAACGCCATGG 1559–1560 1.000 80.2
psbD-trnT-GGU_p4 psbD-trnT-GGU CCACAAAAACGAAACGGTCC GTGGTAGAGTAACGCCATGG 1560–1561 1.000 80.2
psbD-trnT-GGU_p5 psbD-trnT-GGU CCCACAAAAACGAAACGGTC GTGGTAGAGTAACGCCATGG 1561–1562 1.000 80.2

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
Periandra coccinea PV870774.1 153056 View on NCBI ↗
Periandra mediterranea NC_067529.1 153613 View on NCBI ↗