Markers + reference

Meristotropis

2 species · Fabaceae · Fabales

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Species 2
Genome length 128–128 kb
Candidate markers 226
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 226 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rbcL Genome 1082 0.0170 0.98 70.5 yes View details
trnS-UGA-psbC Genome 211 0.0476 1.00 65.4 yes View details
psbC Genome 1422 0.0028 1.00 45.5 yes View details
psbD-trnT-GGU Genome 1451 0.0097 1.00 61.2 yes View details
petN-trnC-GCA Genome 1068 0.0169 1.00 60.7 yes View details
atpI-atpH Genome 1020 0.0134 0.95 70.0 yes View details
atpA-trnR-UCU Genome 255 0.0200 0.98 58.6 yes View details
trnR-UCU-trnG-UCC Genome 348 0.0302 0.95 68.7 yes View details
trnQ-UUG-accD Genome 1213 0.0141 1.00 56.1 yes View details
trnR-ACG-trnN-GUU Genome 545 0.0320 0.98 70.0 yes View details
ycf1-rps15 Genome 544 0.0187 0.99 68.5 yes View details
ndhI-ndhG Genome 469 0.0192 1.00 52.1 yes View details
trnL-UAG-rpl32 Genome 677 0.0225 0.92 60.7 yes View details
trnW-CCA-trnP-UGG Genome 179 0.0391 1.00 75.0 yes View details
trnL-UAA-trnT-UGU Genome 1629 0.0071 0.95 67.0 yes View details
ndhF-trnH-GUG Genome 226 0.0133 0.99 66.4 no View details
atpH-atpF Genome 503 0.0142 0.98 66.0 yes View details
ycf3-psaA Genome 896 0.0069 0.97 65.6 yes View details
trnV-UAC-ndhC Genome 455 0.0176 1.00 63.9 yes View details
accD Genome 1485 0.0088 1.00 63.8 yes View details
ycf2-trnL-CAA Genome 506 0.0119 1.00 63.6 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
trnK-UUU-rbcL_p1 trnK-UUU-rbcL TGGAGTCGCACTTAAAAGCC CGTCAAGCTTGCAAATGGAG 1223–1227 1.000 78.6
trnK-UUU-rbcL_p2 trnK-UUU-rbcL TGGAGTCGCACTTAAAAGCC AGTCCTGAATTAGCTGCTGC 1205–1209 1.000 78.6
trnK-UUU-rbcL_p3 trnK-UUU-rbcL AACCCTACCGATGGTATGGA CGTCAAGCTTGCAAATGGAG 1276–1280 1.000 78.5
trnK-UUU-rbcL_p4 trnK-UUU-rbcL AACCCTACCGATGGTATGGA AGTCCTGAATTAGCTGCTGC 1258–1262 1.000 78.5
trnK-UUU-rbcL_p5 trnK-UUU-rbcL TGGAGTCGCACTTAAAAGCC TTTGAATTCCCGGCAATGGA 1160–1164 1.000 78.4
trnV-UAC-ndhC_p1 trnV-UAC-ndhC AGAAGGTCTACGGTTCGAGT TTCTGGCCCTTTGCTAATCG 605–653 1.000 77.4
trnV-UAC-ndhC_p2 trnV-UAC-ndhC GAAGGTCTACGGTTCGAGTC TTCTGGCCCTTTGCTAATCG 604–652 1.000 74.7
trnV-UAC-ndhC_p3 trnV-UAC-ndhC GTTCGAGTCCGTATAGCCCT TTCTGGCCCTTTGCTAATCG 593–641 1.000 73.6
trnV-UAC-ndhC_p4 trnV-UAC-ndhC AAGGTCTACGGTTCGAGTCC TTCTGGCCCTTTGCTAATCG 603–651 1.000 72.4
trnV-UAC-ndhC_p5 trnV-UAC-ndhC GAGAAGGTCTACGGTTCGAG TTCTGGCCCTTTGCTAATCG 606–654 1.000 72.4
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GCGATGCTCTAACCTCTGAG 1616–1679 1.000 83.1
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GAGTCGAACCGATGACCATC 1647–1710 1.000 82.8
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 1624–1687 1.000 82.6
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GAGTCGAACCGATGACCATC 1655–1718 1.000 82.3
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU AGTCCGTAGCGTCTACCAAT GCGATGCTCTAACCTCTGAG 1630–1693 1.000 81.2
ycf3-psaA_p1 ycf3-psaA AGCCCTTACCCCTGGTAATT TGCCCATTCCTCGAAAGAAG 1021–1044 1.000 81.6
ycf3-psaA_p2 ycf3-psaA AGCCCTTACCCCTGGTAATT GCCCATTCCTCGAAAGAAGT 1020–1043 1.000 81.6
ycf3-psaA_p3 ycf3-psaA AGCTATAGCCCTTACCCCTG TGCCCATTCCTCGAAAGAAG 1027–1050 1.000 81.4
ycf3-psaA_p4 ycf3-psaA AGCTATAGCCCTTACCCCTG GCCCATTCCTCGAAAGAAGT 1026–1049 1.000 81.4
ycf3-psaA_p5 ycf3-psaA TTGGTTGAAGATCACAGGGC TGCCCATTCCTCGAAAGAAG 985–1008 1.000 81.0
trnS-UGA-psbC_p1 trnS-UGA-psbC GAGAGATGGCTGAGTGGTTG CGTCGTTCCGCGGAATATAT 557–558 1.000 81.3
trnS-UGA-psbC_p2 trnS-UGA-psbC GAGAGATGGCTGAGTGGTTG TCTAAGGGGTCCCAATGGTT 621–622 1.000 81.0
trnS-UGA-psbC_p3 trnS-UGA-psbC CCCACCCCTTCCTTTAATCG CGTCGTTCCGCGGAATATAT 850–851 1.000 80.5
trnS-UGA-psbC_p4 trnS-UGA-psbC CTTCACAAAAGGGCATGCTG CGTCGTTCCGCGGAATATAT 719–720 1.000 80.5
trnS-UGA-psbC_p5 trnS-UGA-psbC GAGAGATGGCTGAGTGGTTG CACTGGACCAGAAGCTTCTC 813–814 1.000 80.4
psbC_p1 psbC GAGAGATGGCTGAGTGGTTG TCTTTGCGCCTAGTTTTGGT 2228–2229 1.000 80.2
psbC_p2 psbC GAGAGATGGCTGAGTGGTTG TGGTTCTTTGCGCCTAGTTT 2232–2233 1.000 80.2
psbC_p3 psbC GAGAGATGGCTGAGTGGTTG TTGGTTCTTTGCGCCTAGTT 2233–2234 1.000 80.2
psbC_p4 psbC GAGAGATGGCTGAGTGGTTG GGGCCAATTGCTGTTTTTGT 2289–2290 1.000 80.1
psbC_p5 psbC GAGAGATGGCTGAGTGGTTG TGGGCCAATTGCTGTTTTTG 2290–2291 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
Meristotropis bucharica MT120799.1 127566 View on NCBI ↗
Meristotropis xanthioides MT120806.1 127735 View on NCBI ↗