Markers + reference

Sophora

9 species · Fabaceae · Fabales

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Species 9
Genome length 154–158 kb
Candidate markers 263
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 272 0.0883 0.98 73.4 yes View details
trnK-UUU-rbcL LSC 938 0.0551 0.98 84.0 yes View details
trnG-UCC-trnS-GCU LSC 734 0.0577 0.95 77.1 yes View details
trnT-UGU-trnL-UAA LSC 1278 0.0572 0.97 82.7 yes View details
petN-psbM LSC 1145 0.0508 0.99 78.9 yes View details
trnS-UGA-psbZ LSC 370 0.0573 0.97 79.5 yes View details
psbZ-trnG-GCC LSC 396 0.0628 0.99 82.3 yes View details
psaJ-rpl33 LSC 436 0.0464 1.00 79.8 yes View details
rps11-rpl36 LSC 424 0.0558 0.95 73.2 yes View details
rps3-rps19 LSC 598 0.0465 0.97 78.3 yes View details
ndhF-rpl32 SSC 680 0.0356 0.99 77.9 yes View details
rpl32-trnL-UAG SSC 347 0.0691 0.94 74.4 yes View details
rps15-ycf1 SSC 408 0.0629 0.99 74.3 yes View details
ycf3-trnS-GGA LSC 270 0.0405 1.00 82.3 yes View details
ndhJ-trnC-GCA LSC 1174 0.0380 0.99 80.1 yes View details
trnP-GGG-psaJ LSC 533 0.0451 0.98 80.1 yes View details
trnT-GGU-psbD LSC 1447 0.0330 0.99 78.1 yes View details
trnL-UAA-trnF-GAA LSC 446 0.0473 0.94 77.6 yes View details
ccsA-ndhD SSC 257 0.0516 0.99 74.4 yes View details
trnV-UAC-ndhC LSC 389 0.0559 1.00 74.2 yes View details
psbA-trnK-UUU LSC 257 0.0366 1.00 74.1 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCGAGGCTCCATCTATAAATGG 245–350 1.000 68.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCGAGGCTCCATCTATAAATGG 259–364 1.000 68.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TCGAGGCTCCATCTATAAATGG 258–363 1.000 68.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TCGAGGCTCCATCTATAAATGG 260–365 1.000 68.5
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC TCGAGGCTCCATCTATAAATGG 274–379 1.000 65.7
psbA-trnK-UUU_p1 psbA-trnK-UUU GCTCTCGCGTCTCTCTAAAA ACTAGTTCCGGGTTCGAGTC 281–326 1.000 81.0
psbA-trnK-UUU_p2 psbA-trnK-UUU GCTCTCGCGTCTCTCTAAAA GACTAGTTCCGGGTTCGAGT 282–327 1.000 81.0
psbA-trnK-UUU_p3 psbA-trnK-UUU GCTCTCGCGTCTCTCTAAAA ATCCGACTAGTTCCGGGTTC 286–331 1.000 80.5
psbA-trnK-UUU_p4 psbA-trnK-UUU TACAGAAGCGACCCCATAGG ACTAGTTCCGGGTTCGAGTC 306–351 1.000 80.3
psbA-trnK-UUU_p5 psbA-trnK-UUU TACAGAAGCGACCCCATAGG GACTAGTTCCGGGTTCGAGT 307–352 1.000 80.2
trnK-UUU-rbcL_p1 trnK-UUU-rbcL AGCTTTTCCCACATCAAGCA AATGAGGGACGTGATCTTGC 1153–1505 1.000 91.8
trnK-UUU-rbcL_p2 trnK-UUU-rbcL AGCTTTTCCCACATCAAGCA GCCGTAGCTAATCGAGTAGC 1198–1550 1.000 91.7
trnK-UUU-rbcL_p3 trnK-UUU-rbcL AGCTTTTCCCACATCAAGCA AGTCCTGAATTAGCTGCTGC 1093–1445 1.000 91.7
trnK-UUU-rbcL_p4 trnK-UUU-rbcL AGCTTTTCCCACATCAAGCA GAGGCTAGCAAATGGAGTCC 1108–1460 1.000 91.7
trnK-UUU-rbcL_p5 trnK-UUU-rbcL AGCTTTTCCCACATCAAGCA GCTTGTGAAGTGTGGAAGGA 1376–1427 0.889 86.4
trnV-UAC-ndhC_p1 trnV-UAC-ndhC AAAGGGTTGAGACGCCAAAT GCCTAGGACTAGATCGTGGT 1506–1508 0.333 53.2
trnV-UAC-ndhC_p2 trnV-UAC-ndhC AAAGGGTTGAGACGCCAAAT TGCCTAGGACTAGATCGTGG 1507–1509 0.333 53.2
trnV-UAC-ndhC_p3 trnV-UAC-ndhC AAAGGGTTGAGACGCCAAAT TTCATAGTTACTGTGCCCGC 1546–1548 0.333 53.2
trnV-UAC-ndhC_p4 trnV-UAC-ndhC AAAGGGTTGAGACGCCAAAT AGAGAAGCGGCCATAAACTG 1410–1412 0.333 53.1
trnV-UAC-ndhC_p5 trnV-UAC-ndhC AAAGGGTTGAGACGCCAAAT TACATCGAAGCTCATTGCCC 1155–1157 0.333 53.0
ndhJ-trnC-GCA_p1 ndhJ-trnC-GCA TAGCACCAGGGGGAATGTTA CCGATTAGATCCGATCCGTG 1892–1963 0.889 82.0
ndhJ-trnC-GCA_p2 ndhJ-trnC-GCA AAATGCAGGGTCGTTTGTCT CCGATTAGATCCGATCCGTG 2069–2140 0.889 81.5
ndhJ-trnC-GCA_p3 ndhJ-trnC-GCA TAGCACCAGGGGGAATGTTA CGATTAGATCCGATCCGTGG 1891–1921 0.444 60.6
ndhJ-trnC-GCA_p4 ndhJ-trnC-GCA AAATGCAGGGTCGTTTGTCT CGATTAGATCCGATCCGTGG 2068–2098 0.444 60.3
ndhJ-trnC-GCA_p5 ndhJ-trnC-GCA TTCCCAATGTGCCTATGACG CGATTAGATCCGATCCGTGG 1911–1914 0.333 51.3
trnG-UCC-trnS-GCU_p1 trnG-UCC-trnS-GCU ACGAATCGCACTTTTACCACT CAATCCGACGCTTTAGTCCA 204–806 1.000 82.1
trnG-UCC-trnS-GCU_p2 trnG-UCC-trnS-GCU ACGAATCGCACTTTTACCACT AATCCGACGCTTTAGTCCAC 203–805 1.000 82.1
trnG-UCC-trnS-GCU_p3 trnG-UCC-trnS-GCU ACGAATCGCACTTTTACCAC CAATCCGACGCTTTAGTCCA 204–806 1.000 82.0
trnG-UCC-trnS-GCU_p4 trnG-UCC-trnS-GCU ACGAATCGCACTTTTACCAC AATCCGACGCTTTAGTCCAC 203–805 1.000 82.0
trnG-UCC-trnS-GCU_p5 trnG-UCC-trnS-GCU TCCATAGAACGAATCGCACT CAATCCGACGCTTTAGTCCA 212–814 1.000 82.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Sophora albescens MW940392.1 154797 View on NCBI ↗
Sophora davidii MW940400.1 153622 View on NCBI ↗
Sophora dunii MW940393.1 154872 View on NCBI ↗
Sophora macrocarpa NC_057683.1 154426 View on NCBI ↗
Sophora prazeri MW940396.1 155387 View on NCBI ↗
Sophora tomentosa MW940397.1 155086 View on NCBI ↗
Sophora toromiro NC_057682.1 154260 View on NCBI ↗
Sophora velutina MW940398.1 154707 View on NCBI ↗
Sophora wilsonii MW940399.1 158087 View on NCBI ↗