Markers + reference

Zabelia

6 species · Caprifoliaceae · Dipsacales

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Species 6
Genome length 157–158 kb
Candidate markers 263
Primer pairs 80

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 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 350 0.0829 0.97 82.6 yes View details
accD LSC 2846 0.0459 0.97 77.7 yes View details
ycf2 IRb 7229 0.0094 0.99 51.2 yes View details
trnR-ACG-trnN-GUU IRb 748 0.0660 0.74 77.1 yes View details
trnN-GUU-ndhF SSC 996 0.1220 0.82 77.1 yes View details
ycf1 SSC 5031 0.0188 0.99 54.4 yes View details
trnN-GUU-trnR-ACG IRa 748 0.1412 1.00 82.8 yes View details
trnL-CAA-ycf2 IRa 701 0.0666 0.96 89.4 yes View details
ycf2 IRa 7229 0.0093 1.00 51.8 no View details
ycf2-trnL-CAA IRb 701 0.0660 0.96 89.4 yes View details
rrn16-trnV-GAC IRa 258 0.0416 1.00 88.0 yes View details
trnI-CAU-ycf2 IRb 222 0.0571 0.90 82.2 yes View details
rpl14-rpl16 LSC 215 0.0322 0.97 82.1 yes View details
ycf2-trnI-CAU IRa 222 0.0529 0.90 82.1 yes View details
psbZ-trnG-UCC LSC 323 0.0382 0.99 80.1 yes View details
trnI-CAU-trnH-GUG IRa 547 0.0822 0.91 78.7 no View details
rps12-clpP LSC 158 0.0913 0.99 78.1 yes View details
psaA-ycf3 LSC 802 0.0157 1.00 72.3 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA ACAATCTCAGCAAGTAGGCG GAGCTTAGTTTCCGTCTGGG 1240 0.167 46.4
trnH-GUG-psbA_p2 trnH-GUG-psbA ACAATCTCAGCAAGTAGGCG GAGTGGGAGCTTAGTTTCCG 1246 0.167 46.4
trnH-GUG-psbA_p3 trnH-GUG-psbA ACAATCTCAGCAAGTAGGCG GGAGCTTAGTTTCCGTCTGG 1241 0.167 46.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCTCAGCAAGTAGGCG GGGAGCTTAGTTTCCGTCTG 1242 0.167 46.4
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCTCAGCAAGTAGGCG TCAGTGCTATGCATGGTTCC 1002 0.167 46.2
psbZ-trnG-UCC_p1 psbZ-trnG-UCC TTGCTTCTCCTGATGGTTGG CGTCTTCTCCTTGGCAAAGA 478–483 1.000 82.8
psbZ-trnG-UCC_p2 psbZ-trnG-UCC GCTTCTCCTGATGGTTGGTC CGTCTTCTCCTTGGCAAAGA 476–481 1.000 82.4
psbZ-trnG-UCC_p3 psbZ-trnG-UCC TTGCTTCTCCTGATGGTTGG TACCATTCGACCATATCCGC 451–456 1.000 78.6
psbZ-trnG-UCC_p4 psbZ-trnG-UCC GCTTCTCCTGATGGTTGGTC TACCATTCGACCATATCCGC 449–454 1.000 78.3
psbZ-trnG-UCC_p5 psbZ-trnG-UCC CTCCTGATGGTTGGTCAAGT CGTCTTCTCCTTGGCAAAGA 472–477 1.000 77.6
psaA-ycf3_p1 psaA-ycf3 CCAGGTTTAGCCCATTCCTC ATCAAGCCGCTGAGTATTGG 985–1008 1.000 84.0
psaA-ycf3_p2 psaA-ycf3 CCAGGTTTAGCCCATTCCTC GGAAACAGGCTATAGCGCTT 967–990 1.000 84.0
psaA-ycf3_p3 psaA-ycf3 CCAGGTTTAGCCCATTCCTC TTGGTTGAAGATCACCAGGC 918–941 1.000 83.9
psaA-ycf3_p4 psaA-ycf3 GCCCATTCCTCGAAAGAAGT GGAAACAGGCTATAGCGCTT 958–981 1.000 83.6
psaA-ycf3_p5 psaA-ycf3 GCCCATTCCTCGAAAGAAGT ATCAAGCCGCTGAGTATTGG 976–999 1.000 83.5
accD_p1 accD TTGGAGTTGCGATGAGAGTG CTTAGTCCACACCTGTGCTC 642–982 0.833 84.0
accD_p2 accD TTGGAGTTGCGATGAGAGTG AATGTGAACCCCCTGCTTTT 285–625 0.833 83.8
accD_p3 accD GTTCCGTTTGTGGTGAGAGT CTTAGTCCACACCTGTGCTC 613–759 0.667 77.6
accD_p4 accD GTTCCGTTTGTGGTGAGAGT AAATGTGAACCCCCTGCTTT 257–404 0.667 77.4
accD_p5 accD GTTCCGTTTGTGGTGAGAGT AATGTGAACCCCCTGCTTTT 256–403 0.667 77.4
rps12-clpP_p1 rps12-clpP CTGAACGAGTCGCACATACA ATGCAAGCTGTGAAACCAGA 671–679 1.000 88.8
rps12-clpP_p2 rps12-clpP CTGAACGAGTCGCACATACA TGCAAGCTGTGAAACCAGAT 670–678 1.000 88.8
rps12-clpP_p3 rps12-clpP CTGAACGAGTCGCACATACA TATAAACTCTCCCGGCGGAT 723–731 1.000 88.2
rps12-clpP_p4 rps12-clpP TACACCGGAGCCTTTCCTTA TGCAAGCTGTGAAACCAGAT 1146–1160 0.333 54.8
rps12-clpP_p5 rps12-clpP TACACCGGAGCCTTTCCTTA TATAAACTCTCCCGGCGGAT 1199–1213 0.333 54.7
rpl14-rpl16_p1 rpl14-rpl16 ACACATCAATTCTCGAGCCC CGGGCCGCATACTTTATGAA 382–397 1.000 82.7
rpl14-rpl16_p2 rpl14-rpl16 AGCATATCGGCGATTGCTAG CGGGCCGCATACTTTATGAA 418–433 1.000 82.4
rpl14-rpl16_p3 rpl14-rpl16 CATATCGGCGATTGCTAGCT CGGGCCGCATACTTTATGAA 416–431 1.000 82.4
rpl14-rpl16_p4 rpl14-rpl16 GAGCATATCGGCGATTGCTA CGGGCCGCATACTTTATGAA 419–434 1.000 82.3
rpl14-rpl16_p5 rpl14-rpl16 CCGCTGTTATCCGCTACATT CGGGCCGCATACTTTATGAA 363–378 1.000 82.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Zabelia biflora NC_045063.1 157326 View on NCBI ↗
Zabelia buddleioides MN524628.1 157825 View on NCBI ↗
Zabelia coreana MN524629.1 156714 View on NCBI ↗
Zabelia corymbosa MN524630.1 157325 View on NCBI ↗
Zabelia integrifolia MN524632.1 157551 View on NCBI ↗
Zabelia triflora NC_045053.1 156827 View on NCBI ↗