Markers + reference

Rhus

8 species · Anacardiaceae · Sapindales

Back to catalogue

Species 8
Genome length 159–160 kb
Candidate markers 275
Primer pairs 95

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 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 557 0.0383 0.99 83.3 yes View details
trnK-UUU-rps16 LSC 1109 0.0211 0.96 67.3 yes View details
rps16-trnQ-UUG LSC 1514 0.0152 0.99 67.2 yes View details
trnG-UCC-trnR-UCU LSC 184 0.0289 0.96 56.3 yes View details
trnT-UGU-trnL-UAA LSC 1056 0.0222 0.93 68.6 yes View details
ycf4-cemA LSC 972 0.0258 0.98 64.0 yes View details
rpl22 LSC 486 0.0152 1.00 48.8 yes View details
rpl2 IRb 1490 0.0008 1.00 31.1 no View details
ndhF-rpl32 SSC 963 0.0238 0.97 67.7 yes View details
rpl32-trnL-UAG SSC 1122 0.0346 0.98 77.2 yes View details
ccsA-ndhD SSC 351 0.0375 0.96 72.7 yes View details
ndhD SSC 1503 0.0090 1.00 47.9 yes View details
rpl2 IRa 1490 0.0010 1.00 35.8 yes View details
rpl2-trnH-GUG IRa 156 0.1122 1.00 84.4 no View details
trnD-GUC-trnY-GUA LSC 446 0.0205 0.98 70.1 yes View details
trnR-UCU-atpA LSC 184 0.0350 0.97 67.0 yes View details
ndhC-trnV-UAC LSC 509 0.0109 0.99 65.6 yes View details
trnE-UUC-trnT-GGU LSC 836 0.0163 0.99 65.3 yes View details
rpl22-rps19 LSC 45 0.0833 1.00 62.3 yes View details
accD-psaI LSC 718 0.0130 0.99 61.6 yes View details
rpl33-rps18 LSC 214 0.0196 0.99 61.2 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 532–661 1.000 89.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 546–675 1.000 89.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 545–674 1.000 89.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 547–676 1.000 89.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 581–710 1.000 87.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGGGGTTTTTACGCAGCTTA 1042–1189 1.000 83.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGGGGTTTTTACGCAGCTTA 1041–1188 1.000 83.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGGGGTTTTTACGCAGCTTA 1051–1198 1.000 82.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GGGGGTTTTTACGCAGCTTA 1028–1175 1.000 80.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGGGTTTTTACGCAGCTTAG 1040–1187 1.000 79.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1505–1627 1.000 85.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1516–1638 1.000 85.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1526–1648 1.000 83.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 1527–1649 1.000 83.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCCACAGCTGATCATGTCC GAGGTTCGAATCCTTCCGTC 1528–1650 1.000 81.7
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 256–264 1.000 68.9
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG CCCAAGGTTTAGAAGACCTCTG 266–274 1.000 68.7
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 259–267 1.000 68.7
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG ACCCAAGGTTTAGAAGACCTC 267–275 1.000 68.6
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG CCCAAGGTTTAGAAGACCTCTG 269–277 1.000 68.4
trnR-UCU-atpA_p1 trnR-UCU-atpA ATGAAAGGCGTCCATTGTCT TGGAACGCTTTCTACTTCAGG 295–313 1.000 73.5
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAGGCGTCCATTG TGGAACGCTTTCTACTTCAGG 298–316 1.000 72.9
trnR-UCU-atpA_p3 trnR-UCU-atpA ATGAAAGGCGTCCATTGTCT GGAACGCTTTCTACTTCAGGA 294–312 1.000 71.4
trnR-UCU-atpA_p4 trnR-UCU-atpA GGAATGAAAGGCGTCCATTG GGAACGCTTTCTACTTCAGGA 297–315 1.000 70.8
trnR-UCU-atpA_p5 trnR-UCU-atpA ATGAAAGGCGTCCATTGTCT TCAGGAACATATGGAACGCT 306–324 1.000 70.7
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 500–531 1.000 81.6
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 499–530 1.000 81.6
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 521–552 1.000 80.4
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 520–551 1.000 80.3
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GATTCTTCCTGGGTCGATGC 554–585 1.000 79.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Rhus glabra NC_085283.1 159984 View on NCBI ↗
Rhus hypoleuca MW238820.1 159472 View on NCBI ↗
Rhus integrifolia NC_049060.1 160141 View on NCBI ↗
Rhus ovata NC_049061.1 160262 View on NCBI ↗
Rhus potaninii NC_049131.1 159616 View on NCBI ↗
Rhus punjabensis NC_053824.1 159617 View on NCBI ↗
Rhus typhina NC_046837.1 160204 View on NCBI ↗
Rhus wilsonii MW238821.1 159814 View on NCBI ↗