Markers + reference

Bauhinia

8 species · Fabaceae · Fabales

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Species 8
Genome length 155–157 kb
Candidate markers 268
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 700 0.0464 0.99 74.5 yes View details
rbcL-accD LSC 826 0.0425 0.95 69.7 yes View details
clpP LSC 2182 0.0386 0.99 68.2 yes View details
rps3-rps19 LSC 568 0.0625 1.00 74.6 yes View details
ycf1 IRb 984 0.0451 0.88 67.7 yes View details
ndhF-rpl32 SSC 1021 0.0408 1.00 72.9 yes View details
ycf1 SSC 5256 0.0440 1.00 66.4 no View details
ycf2-trnI-CAU IRa 307 0.1581 0.68 57.1 yes View details
trnH-GUG-psbA LSC 370 0.0539 1.00 72.4 yes View details
psbZ-trnG-GCC LSC 472 0.0493 0.99 72.1 yes View details
ndhG-ndhI SSC 408 0.0521 1.00 72.1 yes View details
trnS-GCU-trnG-UCC LSC 608 0.0409 1.00 71.7 yes View details
trnR-UCU-atpA LSC 394 0.0478 0.99 71.1 yes View details
rpl32-trnL-UAG SSC 358 0.0510 1.00 70.6 yes View details
accD LSC 1521 0.0413 1.00 69.3 yes View details
trnT-UGU-trnL-UAA LSC 869 0.0285 0.97 69.2 yes View details
ycf1-ndhF SSC 71 0.1635 1.00 69.0 yes View details
ndhC-trnV-UAC LSC 561 0.0317 0.99 67.6 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 427–439 1.000 90.4
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CGGTCGAGGCTCCATCTATA 408–420 1.000 89.5
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 476–488 1.000 88.3
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 477–489 1.000 87.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GCCTTGATCCACTTGGCTAC TTCCCTCTAGACCTAGCTGC 432–444 1.000 86.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGATGTCGAGTCAAGAGC CGAAAACTTACAGCGGCTTG 1468–1583 1.000 91.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AACGATGTCGAGTCAAGAGC GAGGTTCGAATCCTTCCGTC 802–877 1.000 91.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACGATGTCGAGTCAAGAGC ATCGAAAACTTACAGCGGCT 1470–1585 1.000 91.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AACGATGTCGAGTCAAGAGC TCGAAAACTTACAGCGGCTT 1469–1584 1.000 90.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTTTTCTCCTCGTACGGC CGAAAACTTACAGCGGCTTG 2080–2193 1.000 90.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC TACCACTAAACTATACCCGC 634–811 1.000 52.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC TTACCACTAAACTATACCCGC 635–812 1.000 52.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC TTTACCACTAAACTATACCCGC 636–813 1.000 52.0
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC CTTTTACCACTAAACTATACCCGC 638–815 1.000 52.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC TTTTACCACTAAACTATACCCGC 637–814 1.000 52.0
trnR-UCU-atpA_p1 trnR-UCU-atpA CCCGCTACCCGCTTATATTC TGAGTTGCTCAAACAGTCCC 992–1036 1.000 91.4
trnR-UCU-atpA_p2 trnR-UCU-atpA CCCGCTACCCGCTTATATTC GAGTTGCTCAAACAGTCCCA 991–1035 1.000 91.3
trnR-UCU-atpA_p3 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG TGAGTTGCTCAAACAGTCCC 1023–1067 1.000 91.0
trnR-UCU-atpA_p4 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG GAGTTGCTCAAACAGTCCCA 1022–1066 1.000 90.9
trnR-UCU-atpA_p5 trnR-UCU-atpA CCCGCTACCCGCTTATATTC CGAAGCTTATCCGGGAGATG 1394–1438 1.000 89.3
psbZ-trnG-GCC_p1 psbZ-trnG-GCC CAACCACTCAGCCATCTCTC CTTGAGGTCACGGGTTCAAA 1299–1401 1.000 90.7
psbZ-trnG-GCC_p2 psbZ-trnG-GCC CAACCACTCAGCCATCTCTC CTTGTGTTTATCGCGGGGTA 1350–1408 0.875 81.9
psbZ-trnG-GCC_p3 psbZ-trnG-GCC CAACCACTCAGCCATCTCTC TTGTGTTTATCGCGGGGTAG 1349–1407 0.875 81.9
psbZ-trnG-GCC_p4 psbZ-trnG-GCC CAACCACTCAGCCATCTCTC CGATCATAGGAGGGTCCCTT 1458–1516 0.875 81.8
psbZ-trnG-GCC_p5 psbZ-trnG-GCC CAACCACTCAGCCATCTCTC CGTTGTTTTTCGACCGGAAG 1622–1680 0.875 81.5
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 889–1051 1.000 89.7
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 897–1059 1.000 89.1
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 921–1083 1.000 88.6
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 929–1091 1.000 88.0
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG AGTCCGTAGCGTCTACCAAT 903–1065 1.000 87.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Bauhinia blakeana MN413506.1 156100 View on NCBI ↗
Bauhinia brachycarpa NC_037762.1 155548 View on NCBI ↗
Bauhinia galpinii PQ826995.1 155397 View on NCBI ↗
Bauhinia monandra PQ826996.1 155351 View on NCBI ↗
Bauhinia purpurea NC_061218.1 156099 View on NCBI ↗
Bauhinia variegata var. candida PQ826993.1 155416 View on NCBI ↗
Bauhinia variegata var. variegata MT176420.1 155415 View on NCBI ↗
Bauhinia yunnanensis PQ433122.1 157382 View on NCBI ↗