Markers + reference

Biancaea

2 species · Fabaceae · Fabales

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Species 2
Genome length 157–160 kb
Candidate markers 255
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 9 remaining regions by MarkerSeek score (out of 255 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 599 0.0389 0.99 75.1 yes View details
psbK-trnS-GCU LSC 695 0.0422 0.99 72.9 yes View details
trnS-GCU-trnG-GCC LSC 655 0.0572 0.99 77.5 yes View details
atpF-atpH LSC 568 0.0401 0.96 77.7 yes View details
psbZ-trnG-UCC LSC 391 0.1264 0.93 86.1 yes View details
trnT-UGU-trnL-UAA LSC 1462 0.0252 0.87 65.0 yes View details
ndhF SSC 2241 0.0089 1.00 47.4 yes View details
ndhF-rpl32 SSC 761 0.0908 0.98 80.4 yes View details
ndhG-ndhI SSC 338 0.1273 0.98 83.6 yes View details
ndhD-psaC SSC 108 0.0648 1.00 72.3 yes View details
rps8-rpl14 LSC 234 0.0565 0.98 69.7 yes View details
rps11-rpl36 LSC 153 0.0458 1.00 68.6 yes View details
ndhC-trnV-UAC LSC 709 0.0341 0.99 66.1 yes View details
trnF-GAA-ndhJ LSC 735 0.0138 0.99 65.9 yes View details
rbcL-accD LSC 927 0.0266 0.97 65.2 yes View details
psbE-petL LSC 860 0.0118 0.99 64.3 yes View details
ccsA-ndhD SSC 311 0.0337 0.95 64.3 yes View details
trnP-UGG-psaJ LSC 420 0.0311 1.00 64.0 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GTCGAATAGAAATGGGGCGT 739–953 1.000 82.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG TCGAATAGAAATGGGGCGTG 738–952 1.000 82.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG TGTCGAATAGAAATGGGGCG 740–954 1.000 82.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 679–893 1.000 82.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GTCGAATAGAAATGGGGCGT 741–955 1.000 81.4
psbK-trnS-GCU_p1 psbK-trnS-GCU CTTTTGTTTGGCAAGCTGCT TGGACTAAAGCGTCGGATTG 803–808 1.000 83.1
psbK-trnS-GCU_p2 psbK-trnS-GCU GTTTGGCAAGCTGCTGTAAG TGGACTAAAGCGTCGGATTG 798–803 1.000 83.1
psbK-trnS-GCU_p3 psbK-trnS-GCU CTTTTGTTTGGCAAGCTGCT GTGGACTAAAGCGTCGGATT 804–809 1.000 83.1
psbK-trnS-GCU_p4 psbK-trnS-GCU GTTTGGCAAGCTGCTGTAAG GTGGACTAAAGCGTCGGATT 799–804 1.000 83.1
psbK-trnS-GCU_p5 psbK-trnS-GCU CTTTTGTTTGGCAAGCTGCT TTTTTCGTACCGAGGGTTCG 766–771 1.000 81.6
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCACT 724–795 1.000 74.8
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 723–794 1.000 74.8
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCAC 724–795 1.000 74.7
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCAC 723–794 1.000 74.7
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA ACGAATCGCACTTTTACCACT 778–849 1.000 73.3
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG TGGGCTGGTTGTAGCATTAG 686–694 1.000 80.6
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG AGGCAGAGGGAAAAATACGG 753–761 1.000 80.1
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG GCAGAGGGAAAAATACGGGG 751–759 1.000 78.6
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GGCAGAGGGAAAAATACGGG 752–760 1.000 78.6
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG CCGAGGCAGAGGGAAAAATA 756–764 1.000 77.8
psbZ-trnG-UCC_p1 psbZ-trnG-UCC GATGGTTGGTCGAGTAACAA GCGTCTTCTCTTTGGCAAAG 538–1072 1.000 63.9
psbZ-trnG-UCC_p2 psbZ-trnG-UCC GATGGTTGGTCGAGTAACAAA GCGTCTTCTCTTTGGCAAAG 538–1072 1.000 62.3
psbZ-trnG-UCC_p3 psbZ-trnG-UCC TGGTTGGTCGAGTAACAAAA GCGTCTTCTCTTTGGCAAAG 536–1070 1.000 61.8
psbZ-trnG-UCC_p4 psbZ-trnG-UCC TGGTTGGTCGAGTAACAAAAA GCGTCTTCTCTTTGGCAAAG 536–1070 1.000 60.3
psbZ-trnG-UCC_p5 psbZ-trnG-UCC GATGGTTGGTCGAGTAACAAAA GCGTCTTCTCTTTGGCAAAG 538–1072 1.000 60.0
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 1392–1512 1.000 84.7
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 1400–1520 1.000 84.1
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 1424–1544 1.000 83.8
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 1432–1552 1.000 83.2
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG AGTCCGTAGCGTCTACCAAT 1406–1526 1.000 82.8

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
Biancaea decapetala NC_088531.1 156813 View on NCBI ↗
Biancaea sappan NC_049085.1 160192 View on NCBI ↗