Markers + reference

Zapoteca

2 species · Fabaceae · Fabales

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Species 2
Genome length 164–180 kb
Candidate markers 266
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1579 0.1356 0.78 82.2 yes View details
trnS-GCU-trnG-UCC LSC 1365 0.1079 0.90 84.8 yes View details
trnT-UGU-trnL-UAA LSC 1467 0.0785 0.81 78.0 yes View details
clpP LSC 2083 0.2538 0.28 65.1 yes View details
rps3-rps19 LSC 763 0.2842 0.86 82.0 yes View details
ycf2 IRb 6828 0.0274 0.98 55.2 yes View details
ccsA-ndhD SSC 588 0.1334 0.98 84.8 yes View details
ycf2 IRa 6828 0.0274 0.98 55.2 no View details
trnI-CAU-rpl23 IRa 165 0.2134 0.99 74.7 yes View details
ndhC-trnV-UAC LSC 926 0.0823 0.92 84.2 yes View details
petA-psbJ LSC 1478 0.0595 0.96 81.7 yes View details
trnS-UGA-psbZ LSC 334 0.0545 0.93 81.6 yes View details
trnR-UCU-atpA LSC 421 0.1054 0.97 81.5 yes View details
rpoB-trnC-GCA LSC 1221 0.0432 0.91 81.0 yes View details
accD-psaI LSC 557 0.1013 0.99 80.6 yes View details
psbE-petL LSC 1287 0.0641 0.86 79.9 yes View details
ndhF-rpl32 SSC 972 0.0763 0.94 79.9 yes View details
rps16-trnQ-UUG LSC 653 0.0881 0.89 79.8 yes View details
psbZ-trnG-GCC LSC 606 0.0534 0.96 79.5 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGCGGGTGTTTTTATGGAAC 1648–1739 1.000 84.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 GAGTCGCACTTAAAAGCCGA GGCGGGTGTTTTTATGGAAC 1649–1740 1.000 84.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GGCGGGTGTTTTTATGGAAC 1646–1737 1.000 83.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC GGCGGGTGTTTTTATGGAAC 1645–1736 1.000 82.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTCGCACTTAAAAGCCGAGT GGCGGGTGTTTTTATGGAAC 1647–1738 1.000 82.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 733–782 1.000 88.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TGATTCCCCCAGATCCACTT GAGGTTCGAATCCTTCCGTC 1073–1126 1.000 87.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GTTCCACGATCCGTTAGCTT GAGGTTCGAATCCTTCCGTC 1208–1260 1.000 87.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CACTCGTATTCGCAACCTCA GAGGTTCGAATCCTTCCGTC 1412 0.500 59.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCCATCATCAAACCCTCCCT GAGGTTCGAATCCTTCCGTC 870 0.500 59.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCACT 1434–1514 1.000 81.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 1433–1513 1.000 81.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCAC 1434–1514 1.000 81.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCAC 1433–1513 1.000 81.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCGCACTTTTACCACT 1488–1568 1.000 79.9
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGCAGAAGCCCTTTTGAAAGA 522–922 1.000 64.3
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GCAGAAGCCCTTTTGAAAGA 521–921 1.000 60.9
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGCAGAAGCCCTTTTGAAAG 522–922 1.000 60.8
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GCAGAAGCCCTTTTGAAAGAA 521–921 1.000 58.8
trnR-UCU-atpA_p5 trnR-UCU-atpA GTTCAAATCCTATTGGACGCA AGCAGAAGCCCTTTTGAAAGA 521–921 1.000 58.6
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ACATTCCCGCATTTACACCC CCGGATTTGAACTGGGGAAA 1255–1311 1.000 82.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ACATTCCCGCATTTACACCC AAAAGGATTTGCAGTCCCCC 1237–1293 1.000 80.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GCATTTACACCCCCAAGCAT CCGGATTTGAACTGGGGAAA 1247–1303 1.000 79.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GACATTCCCGCATTTACACC CCGGATTTGAACTGGGGAAA 1256–1312 1.000 79.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TGTATCTGATTCAACCCGGG CCGGATTTGAACTGGGGAAA 1283–1339 1.000 78.3
trnS-UGA-psbZ_p1 trnS-UGA-psbZ CAACCACTCAGCCATCTCTC CGACCAACCATCAGGAGAAG 437–457 1.000 86.7
trnS-UGA-psbZ_p2 trnS-UGA-psbZ GAGCTATCAACCACTCAGCC CGACCAACCATCAGGAGAAG 444–464 1.000 86.3
trnS-UGA-psbZ_p3 trnS-UGA-psbZ GGAGCTATCAACCACTCAGC CGACCAACCATCAGGAGAAG 445–465 1.000 86.3
trnS-UGA-psbZ_p4 trnS-UGA-psbZ CAAGACCGGAGCTATCAACC CGACCAACCATCAGGAGAAG 452–472 1.000 86.2
trnS-UGA-psbZ_p5 trnS-UGA-psbZ CAACCACTCAGCCATCTCTC CCAACCATCAGGAGAAGCAA 434–454 1.000 85.2

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
Zapoteca formosa PV870735.1 164009 View on NCBI ↗
Zapoteca portoricensis NC_047378.1 180309 View on NCBI ↗