Markers + reference

Abelia

10 species · Caprifoliaceae · Dipsacales

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Species 10
Genome length 157–157 kb
Candidate markers 263
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

12 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 360 0.0446 1.00 74.9 yes View details
trnC-GCA-petN LSC 869 0.0353 1.00 82.2 yes View details
rbcL-accD LSC 1837 0.0520 0.96 83.8 yes View details
rps18 LSC 664 0.0446 0.97 84.7 yes View details
ycf2 IRb 6925 0.0083 1.00 46.5 no View details
ycf2-trnL-CAA IRb 922 0.0135 1.00 59.3 yes View details
GFC95_pgr005-trnR-ACG IRb 261 0.1120 0.99 91.3 yes View details
trnN-GUU-ndhF SSC 1042 0.0292 0.97 75.1 yes View details
trnN-GUU-trnR-ACG IRa 736 0.0277 1.00 75.1 yes View details
trnR-ACG-GFC95_pgr004 IRa 261 0.1116 0.99 91.3 yes View details
trnL-CAA-ycf2 IRa 922 0.0126 1.00 58.6 yes View details
ycf2 IRa 6925 0.0083 1.00 46.6 yes View details
trnE-UUC-trnT-GGU LSC 848 0.0257 0.97 83.3 yes View details
trnH-GUG-trnH-GUG IRa 483 0.0575 1.00 83.3 no View details
rps12-clpP LSC 365 0.0348 1.00 81.0 yes View details
rps15-ycf1 SSC 482 0.0309 1.00 79.1 yes View details
psaA-ycf3 LSC 818 0.0181 0.95 76.4 yes View details
psbJ-psbL LSC 195 0.0336 1.00 76.2 yes View details
trnR-ACG-trnN-GUU IRb 736 0.0283 1.00 75.3 yes View details
ndhC-trnV-UAC LSC 1066 0.0131 0.99 70.8 yes View details
petB-petD LSC 919 0.0125 1.00 69.6 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 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 CAATCCACTGCCTTGATCCA CGGATGTAGCCAAGTGGATC 210–235 1.000 89.9
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TGGATCAAGGCAGTGGATTG 182–207 1.000 89.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CGGATGTAGCCAAGTGGATC 209–234 1.000 89.9
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGATCAAGGCAGTGGATTGT 181–206 1.000 89.9
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG GTGGATCAAGGCAGTGGATT 183–208 1.000 89.9
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 898–933 1.000 88.2
trnC-GCA-petN_p2 trnC-GCA-petN GTATCAATTTGGCGGCATGG AGCCCAAGCGAGACTTACTA 950–985 1.000 87.4
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 916–951 1.000 85.9
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAGAGCCCACTTCTTCCCC 961–996 1.000 83.3
trnC-GCA-petN_p5 trnC-GCA-petN GTATCAATTTGGCGGCATGG TTAGAGCCCACTTCTTCCCC 1013–1048 1.000 82.6
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AACTTCCTTTCGCAGTACCC GAACCGATGACTTACGCCTT 961–992 1.000 86.9
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 916–947 1.000 86.5
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 895–926 1.000 86.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AACTTCCTTTCGCAGTACCC CCGATGACTTACGCCTTACC 958–989 1.000 85.8
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCGATGACTTACGCCTTACC 913–944 1.000 85.4
psaA-ycf3_p1 psaA-ycf3 CCAGGTTTAGCCCATTCCTC ATCAAGCCGCTGAGTATTGG 987–1010 1.000 86.4
psaA-ycf3_p2 psaA-ycf3 CCAGGTTTAGCCCATTCCTC GGAAACAGGCTATAGCGCTT 969–992 1.000 86.4
psaA-ycf3_p3 psaA-ycf3 CCAGGTTTAGCCCATTCCTC TTGGTTGAAGATCACCAGGC 920–943 1.000 86.2
psaA-ycf3_p4 psaA-ycf3 GCCCATTCCTCGAAAGAAGT ATCAAGCCGCTGAGTATTGG 978–1001 1.000 86.0
psaA-ycf3_p5 psaA-ycf3 GCCCATTCCTCGAAAGAAGT GGAAACAGGCTATAGCGCTT 960–983 1.000 86.0
ndhC-trnV-UAC_p1 ndhC-trnV-UAC CGGGGCTAAAACTCCAGAAA AGAAGGTCTACGGTTCGAGT 1179–1221 1.000 81.8
ndhC-trnV-UAC_p2 ndhC-trnV-UAC ATCGGGGCTAAAACTCCAGA AGAAGGTCTACGGTTCGAGT 1181–1223 1.000 79.9
ndhC-trnV-UAC_p3 ndhC-trnV-UAC AATCGGGGCTAAAACTCCAG AGAAGGTCTACGGTTCGAGT 1182–1224 1.000 79.9
ndhC-trnV-UAC_p4 ndhC-trnV-UAC CGGGGCTAAAACTCCAGAAA GAAGGTCTACGGTTCGAGTC 1178–1220 1.000 79.0
ndhC-trnV-UAC_p5 ndhC-trnV-UAC TTCCGGCCCTTTACTAATCG AGAAGGTCTACGGTTCGAGT 1197–1239 1.000 78.4
rbcL-accD_p1 rbcL-accD AATGAGGGACGTGATCTTGC AGGGAGTGGAATCCTGTTCA 2359–2748 1.000 91.4
rbcL-accD_p2 rbcL-accD AATGAGGGACGTGATCTTGC TGAGGGAGTGGAATCCTGTT 2361–2750 1.000 91.4
rbcL-accD_p3 rbcL-accD AATGAGGGACGTGATCTTGC TGCTTGTATGAGGGAGTGGA 2369–2758 1.000 91.4
rbcL-accD_p4 rbcL-accD CGTAGCTAATCGAGTCGCTC AGGGAGTGGAATCCTGTTCA 2402–2791 1.000 91.2
rbcL-accD_p5 rbcL-accD CGTAGCTAATCGAGTCGCTC TGAGGGAGTGGAATCCTGTT 2404–2793 1.000 91.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Abelia chinensis NC_045043.1 157225 View on NCBI ↗
Abelia chinensis var. chinensis MN787751.1 157310 View on NCBI ↗
Abelia chinensis var. ionandra MN787765.1 157438 View on NCBI ↗
Abelia forrestii MN524636.1 157263 View on NCBI ↗
Abelia macrotera MN524637.1 157123 View on NCBI ↗
Abelia macrotera var. deutziifolia MN787767.1 157430 View on NCBI ↗
Abelia macrotera var. macrotera MN787768.1 157305 View on NCBI ↗
Abelia schumannii NC_070274.1 157121 View on NCBI ↗
Abelia uniflora NC_070275.1 157038 View on NCBI ↗
Abelia x grandiflora NC_045054.1 157107 View on NCBI ↗