Markers + reference

Grona

2 species · Fabaceae · Fabales

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Species 2
Genome length 150–150 kb
Candidate markers 264
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rbcL LSC 825 0.0114 0.96 55.9 yes View details
trnT-UGU-rps4 LSC 322 0.0219 0.99 62.3 yes View details
trnG-GCC-psbZ LSC 577 0.0140 0.99 55.4 yes View details
psbD-trnT-GGU LSC 1207 0.0110 0.98 59.8 yes View details
trnE-UUC-psbM LSC 941 0.0150 0.99 56.3 yes View details
trnG-UCC-trnS-GCU LSC 422 0.0220 0.97 60.4 yes View details
rps16-accD LSC 524 0.0174 0.99 64.8 yes View details
ycf4 LSC 605 0.0283 0.99 62.6 yes View details
petA-psbJ LSC 929 0.0121 0.98 58.8 yes View details
psbE-petL LSC 1308 0.0092 1.00 64.3 yes View details
rpl32-trnL-UAG SSC 583 0.0208 0.74 56.1 yes View details
atpF-atpA LSC 80 0.0625 1.00 82.8 yes View details
psbT-psbN LSC 56 0.0536 1.00 81.7 yes View details
pasI-ycf4 LSC 160 0.0625 1.00 75.3 yes View details
ycf3-psaA LSC 627 0.0112 1.00 65.2 yes View details
atpH-atpF LSC 606 0.0084 0.98 65.2 yes View details
trnT-GGU-trnD-GUC LSC 283 0.0189 0.94 63.8 yes View details
clpP LSC 2027 0.0079 1.00 62.7 yes View details
rpl20-rps12 LSC 803 0.0050 1.00 61.7 yes View details
rpoA LSC 1002 0.0050 1.00 61.5 yes View details
rbcL-atpB LSC 757 0.0040 0.99 61.4 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 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 AGAGTCGCTCTTAAAAGCCG GAGCCGTATTTGCCAGAGAA 1513–1543 1.000 82.5
trnK-UUU-rbcL_p2 trnK-UUU-rbcL AGTCGCTCTTAAAAGCCGAG GAGCCGTATTTGCCAGAGAA 1511–1541 1.000 82.5
trnK-UUU-rbcL_p3 trnK-UUU-rbcL GAGTCGCTCTTAAAAGCCGA GAGCCGTATTTGCCAGAGAA 1512–1542 1.000 82.4
trnK-UUU-rbcL_p4 trnK-UUU-rbcL AGAGTCGCTCTTAAAAGCCG AAGAGCCGTATTTGCCAGAG 1515–1545 1.000 82.4
trnK-UUU-rbcL_p5 trnK-UUU-rbcL AGTCGCTCTTAAAAGCCGAG AAGAGCCGTATTTGCCAGAG 1513–1543 1.000 82.4
rbcL-atpB_p1 rbcL-atpB AACACCAGCTTTGAACCCAA CTACATCTAGTACCGGGCCA 905–908 1.000 80.0
rbcL-atpB_p2 rbcL-atpB AACACCAGCTTTGAACCCAA GTTTCAAGCGCAGAAACCTC 855–858 1.000 79.8
rbcL-atpB_p3 rbcL-atpB AACACCAGCTTTGAACCCAA CCTGGGGGAAAAGCTACATC 918–921 1.000 79.5
rbcL-atpB_p4 rbcL-atpB AACACCAGCTTTGAACCCAA ACATCTAGTACCGGGCCAAT 903–906 1.000 78.4
rbcL-atpB_p5 rbcL-atpB GCTTTGAACCCAACACTTGC CTACATCTAGTACCGGGCCA 898–901 1.000 77.7
trnT-UGU-rps4_p1 trnT-UGU-rps4 CTCAGAGGTTAGAGCATCGC AGGTCCTCTGTAACGTGACA 406–409 1.000 80.6
trnT-UGU-rps4_p2 trnT-UGU-rps4 ATGGTCATCGGTTCGAATCC AGGTCCTCTGTAACGTGACA 374–377 1.000 79.9
trnT-UGU-rps4_p3 trnT-UGU-rps4 CGGTTATGTTAGCCCGCTTA AGGTCCTCTGTAACGTGACA 427–430 1.000 79.8
trnT-UGU-rps4_p4 trnT-UGU-rps4 CTCAGAGGTTAGAGCATCGC CTGCCGGCCTTTTACTAGTT 467–470 1.000 79.6
trnT-UGU-rps4_p5 trnT-UGU-rps4 CGGTTATGTTAGCCCGCTTA CTGCCGGCCTTTTACTAGTT 488–491 1.000 78.8
ycf3-psaA_p1 ycf3-psaA AGCCCTTACCCCCAGTAATT ATGACCTGGTTTTGCCCATT 787 1.000 80.5
ycf3-psaA_p2 ycf3-psaA AGCCCTTACCCCCAGTAATT AATGACCTGGTTTTGCCCAT 788 1.000 80.4
ycf3-psaA_p3 ycf3-psaA AAGTTGCGGAGTCTTGGTTT AATGACCTGGTTTTGCCCAT 840 1.000 80.0
ycf3-psaA_p4 ycf3-psaA AAGTTGCGGAGTCTTGGTTT ATGACCTGGTTTTGCCCATT 839 1.000 80.0
ycf3-psaA_p5 ycf3-psaA AGCCCTTACCCCCAGTAATT TGCCCATTCCTCGAAAGAAG 775 1.000 79.8
trnG-GCC-psbZ_p1 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA AGTGGGTATTCTTAATTCTCTCA 655–657 1.000 41.6
trnG-GCC-psbZ_p2 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA AGTGGGTATTCTTAATTCTCTCAT 655–657 1.000 41.6
trnG-GCC-psbZ_p3 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA GTGGGTATTCTTAATTCTCTCA 654–656 1.000 41.6
trnG-GCC-psbZ_p4 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA AGTGGGTATTCTTAATTCTCTCATT 655–657 1.000 41.6
trnG-GCC-psbZ_p5 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA AGTGGGTATTCTTAATTCTCTC 655–657 1.000 41.6
psbD-trnT-GGU_p1 psbD-trnT-GGU CACAAAAACGAAACGGTCCC GTGGTAGAGTAACGCCATGG 1358–1362 1.000 80.3
psbD-trnT-GGU_p2 psbD-trnT-GGU CCACAAAAACGAAACGGTCC GTGGTAGAGTAACGCCATGG 1359–1363 1.000 80.3
psbD-trnT-GGU_p3 psbD-trnT-GGU CCCACAAAAACGAAACGGTC GTGGTAGAGTAACGCCATGG 1360–1364 1.000 80.3
psbD-trnT-GGU_p4 psbD-trnT-GGU CACAAAAACGAAACGGTCCC TCAGTGGTAGAGTAACGCCA 1361–1365 1.000 80.1
psbD-trnT-GGU_p5 psbD-trnT-GGU CCACAAAAACGAAACGGTCC TCAGTGGTAGAGTAACGCCA 1362–1366 1.000 80.1

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
Grona heterocarpos NC_044113.1 149696 View on NCBI ↗
Grona triflora NC_080966.1 149558 View on NCBI ↗