Markers + reference

Diabelia

5 species · Caprifoliaceae · Dipsacales

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Species 5
Genome length 157–157 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

13 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
trnH-GUG-psbA LSC 357 0.0536 0.98 78.9 yes View details
trnC-GCA-petN LSC 870 0.0566 0.99 91.0 yes View details
rbcL-accD LSC 3020 0.0407 0.99 73.2 yes View details
petA-psbJ LSC 1021 0.0137 1.00 56.9 yes View details
clpP LSC 369 0.0396 1.00 74.5 yes View details
ycf2 IRb 6900 0.0070 1.00 45.2 yes View details
trnR-ACG-trnN-GUU IRb 731 0.0213 1.00 70.1 yes View details
trnN-GUU-ndhF SSC 1035 0.0422 1.00 82.3 yes View details
rpl32-trnL-UAG SSC 784 0.0276 1.00 65.5 yes View details
trnR-ACG-rrn5 IRa 251 0.0930 1.00 90.3 yes View details
trnL-CAA-ycf2 IRa 1218 0.0149 1.00 56.3 yes View details
ycf2 IRa 6609 0.0052 1.00 41.5 no View details
trnH-GUG-trnH-GUG IRa 522 0.1476 0.86 76.8 no View details
rrn5-trnR-ACG IRb 252 0.0820 0.99 87.8 yes View details
rps12-clpP LSC 369 0.0528 0.97 85.1 yes View details
ndhF-rpl32 SSC 148 0.0626 1.00 77.9 yes View details
psaA-ycf3 LSC 795 0.0227 1.00 77.7 yes View details
trnN-GUU-trnG-UCC IRa 615 0.0375 1.00 75.2 yes View details
ndhC-trnV-UAC LSC 1076 0.0220 0.98 74.1 yes View details
trnH-GUG-ycf2 IRb 218 0.0615 1.00 74.1 yes View details
ycf2-trnH-GUG IRa 218 0.0615 1.00 74.1 yes View details
psbZ-trnG-UCC LSC 317 0.0530 0.99 74.0 yes View details
accD-psaI LSC 583 0.0362 0.98 73.6 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GGTTTGTCTTGTGTCTCCGT CTGACGGTATGCCTCTAGGA 843–1031 0.600 69.0
trnH-GUG-psbA_p2 trnH-GUG-psbA GGTTTGTCTTGTGTCTCCGT GAGCTTAGTTTCCGTCTGGG 955–1143 0.600 68.9
trnH-GUG-psbA_p3 trnH-GUG-psbA GGTTTGTCTTGTGTCTCCGT GAGTGGGAGCTTAGTTTCCG 961–1149 0.600 68.9
trnH-GUG-psbA_p4 trnH-GUG-psbA GGTTTGTCTTGTGTCTCCGT GGAGCTTAGTTTCCGTCTGG 956–1144 0.600 68.9
trnH-GUG-psbA_p5 trnH-GUG-psbA GGTTTGTCTTGTGTCTCCGT GGGAGCTTAGTTTCCGTCTG 957–1145 0.600 68.9
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 855–935 1.000 90.1
trnC-GCA-petN_p2 trnC-GCA-petN GTATCAATTTGGCGGCATGG AGCCCAAGCGAGACTTACTA 907–987 1.000 89.4
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 873–953 1.000 87.9
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAGAGCCCACTTCTTCCCC 918–998 1.000 85.3
trnC-GCA-petN_p5 trnC-GCA-petN GTATCAATTTGGCGGCATGG TTAGAGCCCACTTCTTCCCC 970–1050 1.000 84.4
psbZ-trnG-UCC_p1 psbZ-trnG-UCC CAACCACTCAGCCATCTCTC CTTGAGGTCACGGGTTCAAA 1163–1171 1.000 82.7
psbZ-trnG-UCC_p2 psbZ-trnG-UCC CAACCACTCAGCCATCTCTC CGTTGTTTTTCGACCGGAAG 1465–1473 1.000 82.3
psbZ-trnG-UCC_p3 psbZ-trnG-UCC ATCCCACATGCCCATTTGTT CGTTGTTTTTCGACCGGAAG 1317–1325 1.000 82.3
psbZ-trnG-UCC_p4 psbZ-trnG-UCC TCGTTATGATACCGTCCGGA CGTTGTTTTTCGACCGGAAG 1597–1605 1.000 82.0
psbZ-trnG-UCC_p5 psbZ-trnG-UCC CGTTATGATACCGTCCGGAC CGTTGTTTTTCGACCGGAAG 1596–1604 1.000 81.9
psaA-ycf3_p1 psaA-ycf3 CCAGGTTTAGCCCATTCCTC ATCAAGCCGCTGAGTATTGG 976–991 1.000 83.9
psaA-ycf3_p2 psaA-ycf3 CCAGGTTTAGCCCATTCCTC GGAAACAGGCTATAGCGCTT 958–973 1.000 83.9
psaA-ycf3_p3 psaA-ycf3 CCAGGTTTAGCCCATTCCTC TTGGTTGAAGATCACCAGGC 909–924 1.000 83.8
psaA-ycf3_p4 psaA-ycf3 GCCCATTCCTCGAAAGAAGT GGAAACAGGCTATAGCGCTT 949–964 1.000 83.5
psaA-ycf3_p5 psaA-ycf3 GCCCATTCCTCGAAAGAAGT ATCAAGCCGCTGAGTATTGG 967–982 1.000 83.4
ndhC-trnV-UAC_p1 ndhC-trnV-UAC CGGGGCTAAAACTCCAGAAA AGAAGGTCTACGGTTCGAGT 1178–1208 1.000 83.5
ndhC-trnV-UAC_p2 ndhC-trnV-UAC ATCGGGGCTAAAACTCCAGA AGAAGGTCTACGGTTCGAGT 1180–1210 1.000 81.7
ndhC-trnV-UAC_p3 ndhC-trnV-UAC AATCGGGGCTAAAACTCCAG AGAAGGTCTACGGTTCGAGT 1181–1211 1.000 81.7
ndhC-trnV-UAC_p4 ndhC-trnV-UAC CGGGGCTAAAACTCCAGAAA GAAGGTCTACGGTTCGAGTC 1177–1207 1.000 80.8
ndhC-trnV-UAC_p5 ndhC-trnV-UAC TTCCGGCCCTTTACTAATCG AGAAGGTCTACGGTTCGAGT 1196–1226 1.000 80.1
rbcL-accD_p1 rbcL-accD CATTCGGAGTTGCGATGAGA CTTAGTCCACACCTGTGCTC 559–675 1.000 90.7
rbcL-accD_p2 rbcL-accD ACGACGGTTGTCCTATTTGG TCTCATCGCAACTCCGAATG 853–969 1.000 90.7
rbcL-accD_p3 rbcL-accD CATTCGGAGTTGCGATGAGA CCAAATAGGACAACCGTCGT 767–883 1.000 90.7
rbcL-accD_p4 rbcL-accD ACGACGGTTGTCCTATTTGG CTTAGTCCACACCTGTGCTC 602–718 1.000 90.6
rbcL-accD_p5 rbcL-accD ATTCGGAGTTGCGATGAGAG CTTAGTCCACACCTGTGCTC 558–674 1.000 89.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Diabelia sanguinea NC_045193.1 156842 View on NCBI ↗
Diabelia serrata MK033527.1 156755 View on NCBI ↗
Diabelia spathulata var. spathulata MK033548.1 156810 View on NCBI ↗
Diabelia stenophylla MK033543.1 156856 View on NCBI ↗
Diabelia stenophylla var. tetrasepala MK033553.1 156635 View on NCBI ↗