Markers + reference

Piptanthus

2 species · Fabaceae · Fabales

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Species 2
Genome length 152–152 kb
Candidate markers 265
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 28.4 yes View details
ndhJ-trnC-GCA LSC 991 0.0058 0.70 59.6 yes View details
trnD-GUC-trnY-GUA LSC 477 0.0126 1.00 51.6 yes View details
psbC-trnS-UGA LSC 189 0.0688 1.00 83.6 yes View details
trnS-UGA-lhbA LSC 367 0.0027 1.00 49.8 yes View details
ndhF SSC 2298 0.0044 0.99 60.5 yes View details
ccsA SSC 981 0.0031 1.00 47.9 yes View details
ccsA-ndhD SSC 334 0.0223 0.94 70.4 yes View details
ndhA SSC 2293 0.0053 0.99 60.9 yes View details
rps15-ycf1 SSC 475 0.0112 0.94 67.0 yes View details
trnH-GUG-psbA LSC 191 0.0419 1.00 68.3 yes View details
trnG-UCC-trnfM-CAU LSC 123 0.0250 0.98 66.3 yes View details
rps3-rps19 LSC 553 0.0073 0.99 63.4 yes View details
rps11-rpl36 LSC 329 0.0096 0.95 63.3 yes View details
psaA-ycf3 LSC 768 0.0040 0.98 62.7 yes View details
petA-psbJ LSC 1092 0.0064 1.00 62.4 yes View details
trnR-ACG-trnN-GUU IRb 634 0.0063 1.00 62.4 yes View details
trnN-GUU-trnR-ACG IRa 634 0.0063 1.00 62.4 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TAACCGGGCTAACCTTGGTA 313–374 1.000 80.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TAACCGGGCTAACCTTGGTA 327–388 1.000 80.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TAACCGGGCTAACCTTGGTA 326–387 1.000 80.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TAACCGGGCTAACCTTGGTA 328–389 1.000 80.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGTCGAGGCTCCATCTCTAA 241–302 1.000 78.9
psbA_p1 psbA TGCTCCTTTACTTTTAAAAACTCGT AGAATTCGTGTGCTTGGGAG 1158 1.000 40.0
psbA_p2 psbA TGCTCCTTTACTTTTAAAAACTCGT AGAGAATTCGTGTGCTTGGG 1160 1.000 40.0
psbA_p3 psbA TGCTCCTTTACTTTTAAAAACTCGT GAGAATTCGTGTGCTTGGGA 1159 1.000 40.0
psbA_p4 psbA TGCTCCTTTACTTTTAAAAACTCGT AATTCGTGTGCTTGGGAGTC 1156 1.000 40.0
psbA_p5 psbA TGCTCCTTTACTTTTAAAAACTCGT GAATTCGTGTGCTTGGGAGT 1157 1.000 40.0
ndhJ-trnC-GCA_p1 ndhJ-trnC-GCA TTGGATAGGATGGCCTTTGC ATTTGTATCGTTTTGGCGGC 850–1149 1.000 81.6
ndhJ-trnC-GCA_p2 ndhJ-trnC-GCA TTGGATAGGATGGCCTTTGC AGTTCAAATCTGGGTGTCGC 787–1086 1.000 80.0
ndhJ-trnC-GCA_p3 ndhJ-trnC-GCA TAGGATGGCCTTTGCGTAAG ATTTGTATCGTTTTGGCGGC 845–1144 1.000 79.5
ndhJ-trnC-GCA_p4 ndhJ-trnC-GCA ATGCCCGAAAGTTGGATAGG ATTTGTATCGTTTTGGCGGC 861–1160 1.000 79.4
ndhJ-trnC-GCA_p5 ndhJ-trnC-GCA TAGGATGGCCTTTGCGTAAG AGTTCAAATCTGGGTGTCGC 782–1081 1.000 77.9
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA TATCTATCGGGACTGACGGG CTGGTTCAAATCCAGCTCGG 581–582 1.000 72.3
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA TATCTATCGGGACTGACGGG TCTACGCTGGTTCAAATCCA 587–588 1.000 70.4
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA CTGGTTCAAATCCAGCTCGG 530–531 1.000 70.1
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA TATCTATCGGGACTGACGGG TGGTTCAAATCCAGCTCGG 580–581 1.000 69.6
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA TATCTATCGGGACTGACGGG GTCTACGCTGGTTCAAATCCA 588–589 1.000 69.1
psbC-trnS-UGA_p1 psbC-trnS-UGA TCATTTATGGCACGCAGGAA GAGAGATGGCTGAGTGGTTG 384 1.000 81.6
psbC-trnS-UGA_p2 psbC-trnS-UGA TCATTTATGGCACGCAGGAA GCTGAGTGGTTGATAGCTCC 376 1.000 81.4
psbC-trnS-UGA_p3 psbC-trnS-UGA TCATTTATGGCACGCAGGAA GGCTGAGTGGTTGATAGCTC 377 1.000 81.4
psbC-trnS-UGA_p4 psbC-trnS-UGA TCATTTATGGCACGCAGGAA GGTTGATAGCTCCGGTCTTG 369 1.000 81.4
psbC-trnS-UGA_p5 psbC-trnS-UGA TTTATGGCACGCAGGAAGAG GAGAGATGGCTGAGTGGTTG 381 1.000 80.5
trnS-UGA-lhbA_p1 trnS-UGA-lhbA CGTCGACCAAAAGGAGAGAG CCAACCATCAGGAGAAGCAA 570–571 1.000 78.4
trnS-UGA-lhbA_p2 trnS-UGA-lhbA CAACCACTCAGCCATCTCTC CCAACCATCAGGAGAAGCAA 487–488 1.000 78.4
trnS-UGA-lhbA_p3 trnS-UGA-lhbA GAGCTATCAACCACTCAGCC CCAACCATCAGGAGAAGCAA 494–495 1.000 78.1
trnS-UGA-lhbA_p4 trnS-UGA-lhbA GGAGCTATCAACCACTCAGC CCAACCATCAGGAGAAGCAA 495–496 1.000 78.1
trnS-UGA-lhbA_p5 trnS-UGA-lhbA CAAGACCGGAGCTATCAACC CCAACCATCAGGAGAAGCAA 502–503 1.000 78.0

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
Piptanthus concolor NC_051876.1 152115 View on NCBI ↗
Piptanthus nepalensis NC_056139.1 152285 View on NCBI ↗