Markers + reference

Rhamnus

7 species · Rhamnaceae · Rosales

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Species 7
Genome length 161–161 kb
Candidate markers 265
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 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1009 0.0086 0.98 67.9 yes View details
trnS-GCU-trnG-UCC LSC 1279 0.0088 1.00 63.8 yes View details
trnC-GCA-petN LSC 956 0.0058 1.00 56.5 yes View details
psbZ-trnG-GCC LSC 563 0.0081 1.00 66.4 yes View details
petA-psbJ LSC 1070 0.0077 1.00 52.6 yes View details
psbE-petL LSC 1394 0.0044 0.99 58.5 yes View details
rpl22 LSC 405 0.0035 1.00 32.5 yes View details
ndhF SSC 2253 0.0045 1.00 46.3 yes View details
ndhF-rpl32 SSC 623 0.0089 1.00 57.4 yes View details
rpl32-trnL-UAG SSC 1425 0.0067 1.00 57.0 yes View details
rpl2-trnH-GUG LSC 557 0.0236 0.50 56.9 no View details
rps4-trnT-UGU LSC 464 0.0065 0.98 64.8 yes View details
psaI-ycf4 LSC 472 0.0038 0.96 63.8 yes View details
accD-psaI LSC 741 0.0055 1.00 63.0 yes View details
trnT-GGU-psbD LSC 1328 0.0037 1.00 62.9 yes View details
atpH-atpI LSC 1212 0.0012 0.99 62.8 yes View details
trnD-GUC-trnY-GUA LSC 462 0.0056 1.00 61.2 yes View details
ndhC-trnV-UAC LSC 522 0.0069 1.00 61.0 yes View details
rps16-trnQ-UUG LSC 714 0.0024 1.00 60.1 yes View details
rps19-rpl2 LSC 123 0.1161 1.00 60.0 yes View details
trnT-UGU-trnL-UAA LSC 1231 0.0030 1.00 59.5 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
trnK-UUU_p1 trnK-UUU GGGACTCCCAAGCACATAAA AACTGTTTTGATTGCGCCAG 2918–2935 1.000 76.3
trnK-UUU_p2 trnK-UUU GGGACTCCCAAGCACATAAAT AACTGTTTTGATTGCGCCAG 2918–2935 1.000 72.2
trnK-UUU_p3 trnK-UUU TCGCGTCTCTCTAAAATTGCA AACTGTTTTGATTGCGCCAG 2979–2996 1.000 71.9
trnK-UUU_p4 trnK-UUU GGGACTCCCAAGCACATAAA GCCAGGCAAACCAATCTCTT 2903–2920 1.000 71.5
trnK-UUU_p5 trnK-UUU CGCGTCTCTCTAAAATTGCAG AACTGTTTTGATTGCGCCAG 2978–2995 1.000 69.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC ATTTCAAAGAAAGCGGGGGT 1189–1204 1.000 83.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT ATTTCAAAGAAAGCGGGGGT 1188–1203 1.000 83.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGATGGTATGGACGAATCC ATTTCAAAGAAAGCGGGGGT 1167–1182 1.000 83.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC TCCTGCAAAAAGGAGCTCAG 1230–1245 1.000 82.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT TCCTGCAAAAAGGAGCTCAG 1229–1244 1.000 82.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GTCGAATAGATTTGGGGCGT 863–877 1.000 80.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG TCGAATAGATTTGGGGCGTG 862–876 1.000 80.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG TGTCGAATAGATTTGGGGCG 864–878 1.000 80.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 803–817 1.000 80.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTCGAATAGATTTGGGGCGT 846–860 1.000 79.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TTAATCAAACCGAGGGACCC 1322–1419 1.000 79.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TTAATCAAACCGAGGGACCC 1321–1418 1.000 79.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAAAGTGTCGACGAAAACGG TTAATCAAACCGAGGGACCC 1392–1489 1.000 79.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AAGTGTCGACGAAAACGGAA TTAATCAAACCGAGGGACCC 1390–1487 1.000 78.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGTGTCGACGAAAACGGAAA TTAATCAAACCGAGGGACCC 1389–1486 1.000 78.8
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT GCGAATCCATGGAAGGTCAT 1248–1273 1.000 81.9
atpH-atpI_p2 atpH-atpI GATCCCTTCTACAGCTTGGC GCGAATCCATGGAAGGTCAT 1333–1358 1.000 81.7
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT AACTTTGGCTGCGGCTTATA 1271–1296 1.000 81.1
atpH-atpI_p4 atpH-atpI GATCCCTTCTACAGCTTGGC AACTTTGGCTGCGGCTTATA 1356–1381 1.000 80.9
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA GCGAATCCATGGAAGGTCAT 1249–1274 1.000 80.7
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 1004–1012 1.000 80.0
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 1065–1073 1.000 78.3
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 1022–1030 1.000 77.8
trnC-GCA-petN_p4 trnC-GCA-petN CTTTGTATCGTTTTGGCGGC AGCCCAAGCGAGACTTACTA 1060–1068 1.000 77.5
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGAGTCCACTTCTTCCCCAT 1083–1091 1.000 76.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Rhamnus cathartica NC_068507.1 161149 View on NCBI ↗
Rhamnus erythroxylum NC_088768.1 161108 View on NCBI ↗
Rhamnus globosa NC_057506.1 160642 View on NCBI ↗
Rhamnus leptacantha NC_082339.1 161248 View on NCBI ↗
Rhamnus parvifolia PQ433220.1 161243 View on NCBI ↗
Rhamnus saxatilis PP541884.1 161105 View on NCBI ↗
Rhamnus taquetii NC_045855.1 161205 View on NCBI ↗