Markers + reference

Diervilla

2 species · Caprifoliaceae · Dipsacales

Back to catalogue

Species 2
Genome length 158–159 kb
Candidate markers 269
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 359 0.0000 1.00 54.0 yes View details
rpoC2 LSC 4143 0.0002 1.00 54.0 yes View details
rpoB-trnC-GCA LSC 1282 0.0008 1.00 59.2 yes View details
ndhC LSC 363 0.0000 1.00 22.8 yes View details
ndhC-trnV-UAC LSC 1082 0.0009 1.00 59.3 yes View details
ycf1 IRb 2325 0.0004 0.99 58.7 yes View details
ycf1 SSC 6165 0.0007 0.98 54.4 yes View details
trnI-CAU-ycf2 IRb 500 0.0000 0.95 61.4 yes View details
ycf2-trnI-CAU IRa 500 0.0000 0.95 61.4 yes View details
rps16 LSC 1121 0.0000 0.99 59.4 yes View details
trnP-UGG-psaJ LSC 444 0.0000 1.00 55.7 yes View details
psaI-ycf4 LSC 425 0.0000 1.00 55.3 yes View details
atpA-atpF LSC 55 0.0000 0.98 54.3 yes View details
rpl2 IRa 1178 NA 0.00 46.2 yes View details
rpl2 IRb 1490 0.0000 1.00 40.0 no 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 75 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 CTCTAGACCTAGCCGCTCTT 424–425 1.000 79.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CTCTAGACCTAGCCGCTCTT 438–439 1.000 78.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CTCTAGACCTAGCCGCTCTT 437–438 1.000 78.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CTCTAGACCTAGCCGCTCTT 439–440 1.000 78.9
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TAGACCTAGCCGCTCTTGAA 421–422 1.000 78.0
rps16_p1 rps16 ACGAATAGAACAAGAAAAAGGGA TGTACCGACTGAACCAATGAC 1311–1317 1.000 40.5
rps16_p2 rps16 ACGAATAGAACAAGAAAAAGGGA GTACCGACTGAACCAATGACT 1310–1316 1.000 40.5
rps16_p3 rps16 ACGAATAGAACAAGAAAAAGGGAA TGTACCGACTGAACCAATGAC 1311–1317 1.000 40.5
rps16_p4 rps16 ACGAATAGAACAAGAAAAAGGGA TCAATTCCATACGGGTTCCA 1268–1274 1.000 40.5
rps16_p5 rps16 ACGAATAGAACAAGAAAAAGGG TGTACCGACTGAACCAATGAC 1311–1317 1.000 40.5
trnG-GCC_p1 trnG-GCC GCGAAAAACGTCGACACTTT TGTGTGAGAAAATTTCGGGA 986–987 1.000 57.0
trnG-GCC_p2 trnG-GCC CTCTCTTCGACAAAAAGCGC TGTGTGAGAAAATTTCGGGA 920–921 1.000 55.9
trnG-GCC_p3 trnG-GCC GCGAAAAACGTCGACACTTT TGTGTGAGAAAATTTCGGGAA 986–987 1.000 55.5
trnG-GCC_p4 trnG-GCC GCGAAAAACGTCGACACTTT TTGTGTGAGAAAATTTCGGGA 987–988 1.000 55.5
trnG-GCC_p5 trnG-GCC CTCTCTTCGACAAAAAGCGC TGTGTGAGAAAATTTCGGGAA 920–921 1.000 54.4
atpA-atpF_p1 atpA-atpF ATGCCATCGCCTACTTGAAG ATATTGACATGTTGGGGGCG 211–212 1.000 77.6
atpA-atpF_p2 atpA-atpF ATGCCATCGCCTACTTGAAG GGGGGCGATGAACGAAATAA 198–199 1.000 77.4
atpA-atpF_p3 atpA-atpF ATGCCATCGCCTACTTGAAG GGCGATGAACGAAATAACCG 195–196 1.000 77.2
atpA-atpF_p4 atpA-atpF CAATGCCATCGCCTACTTGA ATATTGACATGTTGGGGGCG 213–214 1.000 75.2
atpA-atpF_p5 atpA-atpF CAATGCCATCGCCTACTTGA GGGGGCGATGAACGAAATAA 200–201 1.000 75.1
rpoC2_p1 rpoC2 CTTGATCCTTGTGGCTCGAA AGTGATTGCTGAGATTCGCG 233 1.000 73.8
rpoC2_p2 rpoC2 TGATCCTTGTGGCTCGAAAG AGTGATTGCTGAGATTCGCG 231 1.000 73.8
rpoC2_p3 rpoC2 CTAGACTGGATCTGCATGGC AGTGATTGCTGAGATTCGCG 206 1.000 73.3
rpoC2_p4 rpoC2 TAGACTGGATCTGCATGGCT AGTGATTGCTGAGATTCGCG 205 1.000 73.1
rpoC2_p5 rpoC2 GGCTCGAAAGGGAGACTAGA AGTGATTGCTGAGATTCGCG 221 1.000 72.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCCCTCATTTCCATCCTGGA CCGGATTTGAACTGGGGAAA 1362 1.000 77.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTTCTTCCATCAAGCCCTGA CCGGATTTGAACTGGGGAAA 1441 1.000 75.4
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AGTTCTTCCATCAAGCCCTG CCGGATTTGAACTGGGGAAA 1442 1.000 75.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCCCTCATTTCCATCCTGGA AAAAGGATTTGCAGTCCCCC 1344 1.000 74.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CTTCCATCAAGCCCTGATCA CCGGATTTGAACTGGGGAAA 1438 1.000 73.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Diervilla lonicera NC_085759.1 159358 View on NCBI ↗
Diervilla sessilifolia NC_064360.1 158329 View on NCBI ↗