Markers + reference

Berchemiella

3 species · Rhamnaceae · Rosales

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Species 3
Genome length 160–160 kb
Candidate markers 266
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 345 0.0116 1.00 57.0 yes View details
trnK-UUU-rps16 LSC 1027 0.0058 1.00 62.6 yes View details
trnS-GCU-trnG-UCC LSC 1156 0.0085 0.98 65.7 yes View details
rpoB-trnC-GCA LSC 1237 0.0065 1.00 63.2 yes View details
psbM-trnD-GUC LSC 469 0.0057 1.00 46.6 yes View details
trnT-UGU-trnL-UAA LSC 1170 0.0048 1.00 58.0 yes View details
psaJ-rpl33 LSC 454 0.0117 1.00 63.2 yes View details
rpoA LSC 996 0.0013 1.00 45.7 yes View details
ndhF-rpl32 SSC 417 0.0096 1.00 61.9 yes View details
rpl32-trnL-UAG SSC 1461 0.0069 0.99 63.9 yes View details
rps15-trnN-GUU SSC 6379 0.0022 1.00 46.3 yes View details
petD-rpoA LSC 209 0.0191 1.00 65.8 yes View details
accD-psaI LSC 760 0.0053 1.00 62.2 yes View details
psbE-petL LSC 1363 0.0032 1.00 61.3 yes View details
rps16-trnQ-UUG LSC 712 0.0056 1.00 61.2 yes View details
atpH-atpI LSC 1177 0.0028 1.00 61.2 yes View details
rpl20-rps12 LSC 818 0.0033 1.00 61.1 yes View details
atpB-rbcL LSC 828 0.0032 1.00 61.0 yes View details
ycf1 IRb 1074 0.0019 1.00 60.7 yes View details
psaA-ycf3 LSC 750 0.0027 1.00 60.6 yes View details
rbcL-accD LSC 831 0.0008 0.99 60.3 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 CCTCTAGACCTAGCTGCTGT 411 1.000 79.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 425 1.000 79.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 424 1.000 79.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 426 1.000 79.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 414 1.000 79.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC ATTTCAAAGAAAGCGGGGGT 1207 1.000 80.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT ATTTCAAAGAAAGCGGGGGT 1206 1.000 80.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC CTTGCAAAAAGGAGCTCAGC 1247 1.000 79.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT CTTGCAAAAAGGAGCTCAGC 1246 1.000 79.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATTTCAAAGAAAGCGGGGGT 1123 1.000 79.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTCGAATAGATTTGGGGCGT 840–845 1.000 79.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TCGAATAGATTTGGGGCGTG 839–844 1.000 79.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TGTCGAATAGATTTGGGGCG 841–846 1.000 79.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 780–785 1.000 79.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GTCGAATAGATTTGGGGCGT 854–859 1.000 77.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TTAATCAAACCGAGGGACCC 1257–1270 1.000 75.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TTAATCAAACCGAGGGACCC 1256–1269 1.000 75.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAAAGTGTCGACGAAAACGG TTAATCAAACCGAGGGACCC 1327–1340 1.000 75.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CCAAAGTGTCGACGAAAACG TTAATCAAACCGAGGGACCC 1328–1341 1.000 75.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGTGTCGACGAAAACGGAAA TTAATCAAACCGAGGGACCC 1324–1337 1.000 75.1
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT GCGAATCCATGGAAGGTCAT 1230–1236 1.000 80.3
atpH-atpI_p2 atpH-atpI GATCCCTTCTACAGCTTGGC GCGAATCCATGGAAGGTCAT 1315–1321 1.000 80.2
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT CCTGTCATGTTCCTTGGCTT 1306–1312 1.000 79.7
atpH-atpI_p4 atpH-atpI GATCCCTTCTACAGCTTGGC CCTGTCATGTTCCTTGGCTT 1391–1397 1.000 79.7
atpH-atpI_p5 atpH-atpI ATAACGGAAGCGGCAGAAAT AACTTTGGCTGCGGCTTATA 1253–1259 1.000 79.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TAAGCCCCGATCAATGAACC CCGGATTTGAACTGGGGAAA 1389–1394 1.000 77.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ACTCTTCTGTTAAGCCCCGA CCGGATTTGAACTGGGGAAA 1399–1404 1.000 77.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GCCCCGATCAATGAACCTAC CCGGATTTGAACTGGGGAAA 1386–1391 1.000 77.0
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AACTCTTCTGTTAAGCCCCG CCGGATTTGAACTGGGGAAA 1400–1405 1.000 76.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AGCCCCGATCAATGAACCTA CCGGATTTGAACTGGGGAAA 1387–1392 1.000 76.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Berchemiella berchemiifolia NC_037477.1 160410 View on NCBI ↗
Berchemiella wilsonii var. pubipetiolata PX776296.1 160317 View on NCBI ↗
Berchemiella wilsonii var. wilsonii KY926621.1 160333 View on NCBI ↗