Markers + reference

Berchemia

5 species · Rhamnaceae · Rosales

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Species 5
Genome length 155–161 kb
Candidate markers 266
Primer pairs 95

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 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 969 0.1222 0.98 84.1 yes View details
rps16-trnQ-UUG LSC 749 0.1322 0.99 85.7 yes View details
trnS-GCU-trnG-UCC LSC 1230 0.0982 0.94 83.5 yes View details
psbZ-trnG-GCC LSC 485 0.1390 1.00 74.9 yes View details
ndhC-trnV-UAC LSC 556 0.1456 0.97 83.1 yes View details
ndhF-rpl32 SSC 386 0.1858 0.92 69.8 yes View details
rpl32-trnL-UAG SSC 1421 0.0879 0.84 76.9 yes View details
ndhA SSC 2269 0.0700 0.99 82.9 yes View details
ycf1 SSC 5757 0.0825 1.00 76.3 yes View details
rpl20-rps12 LSC 819 0.0728 0.99 85.5 yes View details
trnT-GGU-psbD LSC 1150 0.0785 1.00 84.8 yes View details
trnF-GAA-ndhJ LSC 756 0.0713 1.00 84.8 yes View details
matK-trnK-UUU LSC 742 0.0798 1.00 84.7 yes View details
rps16 LSC 1144 0.0726 0.99 84.5 yes View details
petB LSC 1419 0.0542 1.00 84.5 yes View details
rpoB-trnC-GCA LSC 1246 0.0785 1.00 84.3 yes View details
psbM-trnD-GUC LSC 465 0.0652 1.00 84.3 yes View details
clpP LSC 2095 0.0596 1.00 83.6 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU AGCCGTGATCATGAGCAAAT GTCGTCTACAGCCTTTAGCC 1499–1526 0.800 73.6
matK-trnK-UUU_p2 matK-trnK-UUU AGCCGTGATCATGAGCAAAT AGTGCCAATCCAACACAAGT 1431–1447 0.800 73.2
matK-trnK-UUU_p3 matK-trnK-UUU ACTCGTGAAGAAAAAGCCGT GTCGTCTACAGCCTTTAGCC 1931–1958 0.800 73.2
matK-trnK-UUU_p4 matK-trnK-UUU ACTCGTGAAGAAAAAGCCGT AGTGCCAATCCAACACAAGT 1863–1879 0.800 72.8
matK-trnK-UUU_p5 matK-trnK-UUU AGCCGTGATCATGAGCAAAT AATGTTTTGATTGCGCTGGG 988–991 0.800 71.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC ATTTCAAAGAAAGCGGGGGT 1113–1149 0.800 75.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT ATTTCAAAGAAAGCGGGGGT 1112–1148 0.800 75.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 ATTGGTACCACAGTAGGGCT ATTTCAAAGAAAGCGGGGGT 1316–1352 0.800 75.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 ATTGGTACCACAGTAGGGCT CGTTGCAATTGATGTTCGCT 1467–1503 0.800 74.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 ATTGGTACCACAGTAGGGCT TCGTTGCAATTGATGTTCGC 1468–1504 0.800 74.8
rps16_p1 rps16 ACTTGTGTTGGATTGGCACT AGCATACCCAACCCGCTATA 2310–2323 0.800 72.2
rps16_p2 rps16 GGCTAAAGGCTGTAGACGAC AGCATACCCAACCCGCTATA 2226–2244 0.800 71.8
rps16_p3 rps16 ACTTGTGTTGGATTGGCACT CGGCCGAACCAATGACTATT 1617–1647 0.800 71.7
rps16_p4 rps16 TAGAACAGGTAAGGGTGGGG AGCATACCCAACCCGCTATA 2003–2006 0.600 63.4
rps16_p5 rps16 TAGAACAGGTAAGGGTGGGG CGGCCGAACCAATGACTATT 1319–1329 0.600 62.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGATGTCGAGTCAAGAGC CTCAGGTAATTTGGCGACGA 1405–1422 0.800 73.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CTCGAGCTCCATCATGTACG CTCAGGTAATTTGGCGACGA 1478–1491 0.800 73.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACGATGTCGAGTCAAGAGC AGCAGCTTGCCAAACAAAAG 1492–1509 0.800 72.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AACGATGTCGAGTCAAGAGC CTTACAGCAGCTTGCCAAAC 1497–1514 0.800 72.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG CTCAGGTAATTTGGCGACGA 1329–1346 0.800 72.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 849–1299 1.000 63.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 848–1298 1.000 63.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 851–1301 1.000 62.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 850–1300 1.000 62.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACGAATCACACTTTTACCACT 850–1300 1.000 61.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GATACCGGGGCTTTGCAATA CCGGATTTGAACTGGGGAAA 1610–1719 1.000 91.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCGGGGCTTTGCAATATTTG CCGGATTTGAACTGGGGAAA 1606–1715 1.000 90.9
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GATACCGGGGCTTTGCAATA CCCTCTGGCTCTCCAATCTA 1978–1999 0.800 72.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CCGGATTTGAACTGGGGAAA 1815–1835 0.800 72.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CCCTCTGGCTCTCCAATCTA 2094–2115 0.800 72.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Berchemia flavescens MK460212.1 160872 View on NCBI ↗
Berchemia floribunda PQ858236.1 161218 View on NCBI ↗
Berchemia lineata NC_051560.1 154962 View on NCBI ↗
Berchemia polyphylla NC_072275.1 161222 View on NCBI ↗
Berchemia polyphylla var. leioclada OR197706.1 161210 View on NCBI ↗