Markers + reference

Berlinia

2 species · Fabaceae · Fabales

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Species 2
Genome length 158–160 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

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
petN-psbM LSC 1249 0.0073 0.99 63.0 yes View details
trnT-GGU-psbD LSC 1378 0.0104 0.98 66.9 yes View details
psbC-trnS-UGA LSC 234 0.0427 1.00 70.5 yes View details
trnS-UGA-psbZ LSC 378 0.0132 1.00 59.6 yes View details
psbZ-trnG-GCC LSC 634 0.0259 0.97 68.4 yes View details
accD-psaI LSC 541 0.0135 0.96 56.0 yes View details
petA-psbJ LSC 827 0.0097 1.00 49.9 yes View details
rpl20 LSC 363 0.0110 1.00 48.1 yes View details
rps11-rpl36 LSC 379 0.0211 1.00 63.6 yes View details
ndhA SSC 2332 0.0064 1.00 47.8 yes View details
ndhI-ndhG SSC 549 0.1284 0.95 97.5 yes View details
rpl32-ndhF SSC 1012 0.0130 0.99 53.8 yes View details
trnG-GCC-trnfM-CAU LSC 157 0.0423 0.90 76.0 yes View details
trnR-UCU-atpA LSC 414 0.0154 0.94 68.2 yes View details
trnF-GAA-ndhJ LSC 753 0.0070 0.95 67.5 yes View details
psbL-psbF LSC 22 0.0455 1.00 67.2 yes View details
trnR-ACG-trnN-GUU IRb 703 0.0101 0.98 66.2 yes View details
trnN-GUU-trnR-ACG IRa 703 0.0101 0.98 66.2 yes View details
rps3-rps19 LSC 717 0.0046 0.92 64.9 yes View details
petL-petG LSC 192 0.0160 0.97 64.2 yes View details
trnC-GCA-petN LSC 1056 0.0058 0.97 63.9 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
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CATTTACCGGGGAAGCAGAA 528–542 1.000 70.1
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AAGACATTTACCGGGGAAGC 532–546 1.000 70.1
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GGAAGCAGAAGCCCTTTTGA 518–532 1.000 68.1
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ATTTACCGGGGAAGCAGAAG 527–541 1.000 67.7
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT CATTTACCGGGGAAGCAGAA 563–577 1.000 67.0
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 1091–1112 1.000 80.5
trnC-GCA-petN_p2 trnC-GCA-petN TTTATCGTTTTGGCGGCATG AGCCCAAGCGAGACTTACTA 1144–1165 1.000 78.9
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TCTTCCCCATACTACGAGGG 1142–1163 1.000 78.6
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 1109–1130 1.000 78.3
trnC-GCA-petN_p5 trnC-GCA-petN TTTATCGTTTTGGCGGCATG TCTTCCCCATACTACGAGGG 1195–1216 1.000 77.0
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 1405–1412 1.000 68.8
petN-psbM_p2 petN-psbM CCCTCGTAGTATGGGGAAGA TGCTACTGCACTGTTCATTCT 1354–1361 1.000 67.0
petN-psbM_p3 petN-psbM TCCCTCGTAGTATGGGGAAG TGCTACTGCACTGTTCATTCT 1355–1362 1.000 67.0
petN-psbM_p4 petN-psbM GGGGGCATAATTCACATGGA TGCTACTGCACTGTTCATTCT 1427–1434 1.000 66.9
petN-psbM_p5 petN-psbM AGGGGGCATAATTCACATGG TGCTACTGCACTGTTCATTCT 1428–1435 1.000 66.9
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1505–1528 1.000 79.9
trnT-GGU-psbD_p2 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GACCGGACCAACCTACAAAA 1519–1542 1.000 79.8
trnT-GGU-psbD_p3 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1508–1531 1.000 79.7
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GACCGGACCAACCTACAAAA 1522–1545 1.000 79.6
trnT-GGU-psbD_p5 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG TAGACCGGACCAACCTACAA 1521–1544 1.000 79.4
psbC-trnS-UGA_p1 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GAGAGATGGCTGAGTGGTTG 399 1.000 78.8
psbC-trnS-UGA_p2 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GCTGAGTGGTTGATAGCTCC 391 1.000 78.6
psbC-trnS-UGA_p3 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GGCTGAGTGGTTGATAGCTC 392 1.000 78.6
psbC-trnS-UGA_p4 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GGTTGATAGCTCCGGTCTTG 384 1.000 78.6
psbC-trnS-UGA_p5 psbC-trnS-UGA TAGGTCATTTATGGCACGCG GAGAGATGGCTGAGTGGTTG 433 1.000 78.3
trnS-UGA-psbZ_p1 trnS-UGA-psbZ CAACCACTCAGCCATCTCTC CGACCAACCATCAGGAGAAG 501–502 1.000 80.5
trnS-UGA-psbZ_p2 trnS-UGA-psbZ GAGCTATCAACCACTCAGCC CGACCAACCATCAGGAGAAG 508–509 1.000 80.2
trnS-UGA-psbZ_p3 trnS-UGA-psbZ GGAGCTATCAACCACTCAGC CGACCAACCATCAGGAGAAG 509–510 1.000 80.2
trnS-UGA-psbZ_p4 trnS-UGA-psbZ CAAGACCGGAGCTATCAACC CGACCAACCATCAGGAGAAG 516–517 1.000 80.2
trnS-UGA-psbZ_p5 trnS-UGA-psbZ TTCGTCGAGCAAAAGGAGAG CGACCAACCATCAGGAGAAG 586–587 1.000 80.0

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
Berlinia bruneelii PV870699.1 159549 View on NCBI ↗
Berlinia grandiflora PV870710.1 158128 View on NCBI ↗