Markers + reference

Pentaclethra

2 species · Fabaceae · Fabales

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Species 2
Genome length 159–160 kb
Candidate markers 270
Primer pairs 75

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 7 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 IRb 770 0.0026 1.00 56.2 no View details
ndhF SSC 2238 0.4654 0.87 79.8 yes View details
ccsA SSC 972 0.4768 0.75 78.1 yes View details
ndhD SSC 1506 0.4755 0.85 80.9 yes View details
psaC SSC 246 0.4934 0.92 76.7 yes View details
ndhA SSC 2443 0.4554 0.85 78.9 yes View details
ndhH SSC 1182 0.5021 0.82 80.1 yes View details
rps15 SSC 267 0.4722 0.94 77.4 yes View details
ycf1 SSC 5328 0.3809 0.90 76.1 yes View details
petB-petD LSC 191 0.0824 0.95 89.4 yes View details
ndhI SSC 486 0.4665 0.92 80.4 yes View details
ndhC-trnV-UAC LSC 602 0.0776 0.96 80.2 yes View details
ndhF-rpl32 SSC 911 0.4269 0.83 80.1 yes View details
rps15-ycf1 SSC 394 0.4380 0.88 77.5 yes View details
ndhG-ndhI SSC 426 0.4356 0.86 77.4 yes View details
ndhD-psaC SSC 116 0.5946 0.96 76.7 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ndhC-trnV-UAC_p1 ndhC-trnV-UAC AGAGAAGCGGCCATAAACTG AAAAGATGCACGTTGGGTCT 1224–1225 1.000 84.2
ndhC-trnV-UAC_p2 ndhC-trnV-UAC CGCACTAAAGAAGGAGCCAT AAAAGATGCACGTTGGGTCT 1381–1382 1.000 83.7
ndhC-trnV-UAC_p3 ndhC-trnV-UAC CGTGGTACCAGTCCATAACG AAAAGATGCACGTTGGGTCT 1306–1307 1.000 83.5
ndhC-trnV-UAC_p4 ndhC-trnV-UAC TGGTTCAGGCATTTGCTCAT AAAAGATGCACGTTGGGTCT 1406–1407 1.000 83.3
ndhC-trnV-UAC_p5 ndhC-trnV-UAC AGAGAAGCGGCCATAAACTG GCACAAGGGCTATAGCTCAG 1815–1816 1.000 81.9
petB-petD_p1 petB-petD TAAGCAAGGCATTTCCGGTC GTTCAAGTCACACACTCCCA 240–247 1.000 81.0
petB-petD_p2 petB-petD TAAGCAAGGCATTTCCGGTC AAGTCATATATCTGCGCGGC 270–277 1.000 80.4
petB-petD_p3 petB-petD CAAGGCATTTCCGGTCCTTT GTTCAAGTCACACACTCCCA 236–243 1.000 79.5
petB-petD_p4 petB-petD CAAGGCATTTCCGGTCCTTT AAGTCATATATCTGCGCGGC 266–273 1.000 78.9
petB-petD_p5 petB-petD GTAAGCAAGGCATTTCCGGT AAGTCATATATCTGCGCGGC 271–278 1.000 78.1
ndhF_p1 ndhF TGTTTCGATGCAACAACCAA TCAAAAGAGATCAAATTGGCGA 2827 0.500 23.1
ndhF_p2 ndhF ATGTTTCGATGCAACAACCA TCAAAAGAGATCAAATTGGCGA 2828 0.500 21.3
ndhF_p3 ndhF TGTTTCGATGCAACAACCAA TCAAAAGAGATCAAATTGGCGAA 2827 0.500 20.5
ndhF_p4 ndhF TGTTTCGATGCAACAACCAA TTCAAAAGAGATCAAATTGGCGA 2828 0.500 20.5
ndhF_p5 ndhF TGTTTCGATGCAACAACCAA TGGCGAATAAGAAACAAAACTCA 2811 0.500 20.0
ndhF-rpl32_p1 ndhF-rpl32 AAAACGCTAGGAAAAGCCCA AGCGTGTCTACCGATTTCAC 1661 0.500 59.9
ndhF-rpl32_p2 ndhF-rpl32 AAAACGCTAGGAAAAGCCCA CAGCGTGTCTACCGATTTCA 1662 0.500 59.8
ndhF-rpl32_p3 ndhF-rpl32 AAAACGCTAGGAAAAGCCCA AGCCAATTCCAAAATGGGGT 1485 0.500 59.6
ndhF-rpl32_p4 ndhF-rpl32 TAGGGCGTGTGAACCAAAAA AGCGTGTCTACCGATTTCAC 2032 0.500 59.5
ndhF-rpl32_p5 ndhF-rpl32 TAGGGCGTGTGAACCAAAAA CAGCGTGTCTACCGATTTCA 2033 0.500 59.5
ccsA_p1 ccsA GTGAAATCGGTAGACACGCT GGTATGAGCGGTTTTGTTGC 1763 0.500 59.8
ccsA_p2 ccsA TGAAATCGGTAGACACGCTG GGTATGAGCGGTTTTGTTGC 1762 0.500 59.7
ccsA_p3 ccsA ACCCCATTTTGGAATTGGCT GGTATGAGCGGTTTTGTTGC 1939 0.500 59.5
ccsA_p4 ccsA GTGAAATCGGTAGACACGCT GGTGTTTGTGAGAACCCCTT 1280 0.500 59.4
ccsA_p5 ccsA TGAAATCGGTAGACACGCTG GGTGTTTGTGAGAACCCCTT 1279 0.500 59.4
ndhD_p1 ndhD AATGAGGCCTGGGGATCATA TCTGCTCCAAGAACAGAGGA 2270 0.500 58.8
ndhD_p2 ndhD TAATGAGGCCTGGGGATCAT TCTGCTCCAAGAACAGAGGA 2271 0.500 58.8
ndhD_p3 ndhD TGAGGCCTGGGGATCATATT TCTGCTCCAAGAACAGAGGA 2268 0.500 58.8
ndhD_p4 ndhD AATGAGGCCTGGGGATCATA AAACAACTCGAAGCATGGGT 2176 0.500 58.7
ndhD_p5 ndhD TGAGGCCTGGGGATCATATT AAACAACTCGAAGCATGGGT 2174 0.500 58.7

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
Pentaclethra eetveldeana PV870743.1 159311 View on NCBI ↗
Pentaclethra macroloba PV870734.1 159628 View on NCBI ↗