Markers + reference

Rhopalodia

3 species · Rhopalodiaceae · Rhopalodiales

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Species 3
Genome length 120–121 kb
Candidate markers 328
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 328 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psb30-trnK-UUU Genome 372 0.1150 1.00 83.2 yes View details
trnD-GUC-petM Genome 298 0.1336 1.00 78.3 yes View details
trnfM-CAU-rpl12 Genome 424 0.1737 1.00 82.1 yes View details
trnF-GAA-psbX Genome 603 0.1215 1.00 89.9 yes View details
rps2-rbcS Genome 366 0.1466 1.00 73.9 yes View details
atpA-ycf45 Genome 929 0.1600 1.00 84.5 yes View details
rpl35-psaE Genome 920 0.1559 0.99 82.1 yes View details
rrn5-ycf35 Genome 775 0.1007 0.98 83.7 yes View details
rps16-trnL-UAA Genome 479 0.1461 1.00 82.7 yes View details
ycf35-rrn5 Genome 775 0.1016 0.98 83.7 yes View details
trnT-UGU-trnR-UCU Genome 148 0.1171 1.00 83.6 yes View details
trnE-UUC-trnG-GCC Genome 35 0.1010 0.94 83.0 yes View details
ccsA-psbA Genome 412 0.1181 1.00 80.7 yes View details
rpl32-ycf35 Genome 540 0.1033 1.00 80.7 yes View details
trnK-UUU-psbC Genome 181 0.1510 1.00 80.3 yes View details
ftsH-trnP-UGG Genome 465 0.0552 1.00 80.0 yes View details
trnM-CAU-trnS-GCU Genome 66 0.1566 1.00 78.6 yes View details
rpl27-rpl21 Genome 11 0.0606 1.00 78.2 yes View details
cbbx-psaL Genome 93 0.1362 1.00 78.1 yes View details
trnP-UGG-psaB Genome 253 0.0935 1.00 78.1 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
cbbx-psaL_p1 cbbx-psaL CTCCGCCCATAGCTTTCTTT AGGTCATTTAGCAACGCCAA 879–884 1.000 84.1
cbbx-psaL_p2 cbbx-psaL CTCCGCCCATAGCTTTCTTT TAGCAACGCCAATCACATCA 871–876 1.000 84.0
cbbx-psaL_p3 cbbx-psaL CTCCGCCCATAGCTTTCTTT GCAACGCCAATCACATCATC 869–874 1.000 83.5
cbbx-psaL_p4 cbbx-psaL CTCCGCCCATAGCTTTCTTT AGTGCAAAGCAGAACCCTAC 1155–1156 0.667 66.7
cbbx-psaL_p5 cbbx-psaL CTCCGCCCATAGCTTTCTTT GTGCAAAGCAGAACCCTACT 1154–1155 0.667 66.7
trnE-UUC-trnG-GCC_p1 trnE-UUC-trnG-GCC GAGCTGTCCTAGGCCTCTAG GGGCATAGCTCAGTGGTAGA 134–136 1.000 76.4
trnE-UUC-trnG-GCC_p2 trnE-UUC-trnG-GCC CTGTCCTAGGCCTCTAGACG GGGCATAGCTCAGTGGTAGA 131–133 1.000 76.4
trnE-UUC-trnG-GCC_p3 trnE-UUC-trnG-GCC CTAGGCCTCTAGACGATGGG GGGCATAGCTCAGTGGTAGA 126–128 1.000 76.1
trnE-UUC-trnG-GCC_p4 trnE-UUC-trnG-GCC CCTAGGCCTCTAGACGATGG GGGCATAGCTCAGTGGTAGA 127–129 1.000 76.0
trnE-UUC-trnG-GCC_p5 trnE-UUC-trnG-GCC TGAAAGGGAGCTGTCCTAGG GGGCATAGCTCAGTGGTAGA 141–143 1.000 75.9
psb30-trnK-UUU_p1 psb30-trnK-UUU ACCTGTAGCGATAAGTTGTCC GGGACTCGAACCCAGAACTA 453–488 1.000 76.3
psb30-trnK-UUU_p2 psb30-trnK-UUU AGTTGTCCTAGAACTTGCCA GGGACTCGAACCCAGAACTA 440–475 1.000 75.5
psb30-trnK-UUU_p3 psb30-trnK-UUU ACCTGTAGCGATAAGTTGTCC CGAACCCAGAACTATTCGGT 447–482 1.000 74.5
psb30-trnK-UUU_p4 psb30-trnK-UUU CCTGTAGCGATAAGTTGTCCT GGGACTCGAACCCAGAACTA 452–487 1.000 74.0
psb30-trnK-UUU_p5 psb30-trnK-UUU AGTTGTCCTAGAACTTGCCA CGAACCCAGAACTATTCGGT 434–469 1.000 73.7
trnK-UUU-psbC_p1 trnK-UUU-psbC TGGGGTTGCTAACTCAATGG AACCGTGCTAATGAACCTGT 294–300 1.000 83.7
trnK-UUU-psbC_p2 trnK-UUU-psbC GGGGTTGCTAACTCAATGGT AACCGTGCTAATGAACCTGT 293–299 1.000 83.7
trnK-UUU-psbC_p3 trnK-UUU-psbC TAGTTCTGGGTTCGAGTCCC AACCGTGCTAATGAACCTGT 250–256 1.000 82.1
trnK-UUU-psbC_p4 trnK-UUU-psbC ACCGAATAGTTCTGGGTTCG AACCGTGCTAATGAACCTGT 256–262 1.000 80.3
trnK-UUU-psbC_p5 trnK-UUU-psbC CCGAATAGTTCTGGGTTCGA AACCGTGCTAATGAACCTGT 255–261 1.000 78.0
trnT-UGU-trnR-UCU_p1 trnT-UGU-trnR-UCU GGTTCAAGTCCCTTCACCAG TAGGGCCTATCGTCTAACGG 239–245 1.000 89.3
trnT-UGU-trnR-UCU_p2 trnT-UGU-trnR-UCU GTAGGTTGGGGGTTCAAGTC TAGGGCCTATCGTCTAACGG 249–255 1.000 88.1
trnT-UGU-trnR-UCU_p3 trnT-UGU-trnR-UCU GGTTCAAGTCCCTTCACCAG TTCGATTCCTACTGGGCCTA 184–190 1.000 87.3
trnT-UGU-trnR-UCU_p4 trnT-UGU-trnR-UCU GTAGGTTGGGGGTTCAAGTC TTCGATTCCTACTGGGCCTA 194–200 1.000 86.4
trnT-UGU-trnR-UCU_p5 trnT-UGU-trnR-UCU CTCAATGGTAGAGCAACGGA TAGGGCCTATCGTCTAACGG 279–285 1.000 83.2
trnM-CAU-trnS-GCU_p1 trnM-CAU-trnS-GCU AGTGGTTAGAGCAGGGGATT CTTTCGACCACTCAGCCATT 151 1.000 86.2
trnM-CAU-trnS-GCU_p2 trnM-CAU-trnS-GCU AGTGGTTAGAGCAGGGGATT TTCGACCACTCAGCCATTTC 149 1.000 86.2
trnM-CAU-trnS-GCU_p3 trnM-CAU-trnS-GCU TGGTTAGAGCAGGGGATTCA CTTTCGACCACTCAGCCATT 149 1.000 86.2
trnM-CAU-trnS-GCU_p4 trnM-CAU-trnS-GCU TGGTTAGAGCAGGGGATTCA TTCGACCACTCAGCCATTTC 147 1.000 86.2
trnM-CAU-trnS-GCU_p5 trnM-CAU-trnS-GCU AGTGGTTAGAGCAGGGGATT GACCACTCAGCCATTTCTCC 146 1.000 85.7

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
Rhopalodia fuxianensis PV631713.1 120641 View on NCBI ↗
Rhopalodia inflata PV631711.1 120572 View on NCBI ↗
Rhopalodia yunnanensis PV631712.1 120209 View on NCBI ↗