Markers + reference

Lonicera

80 species · Caprifoliaceae · Dipsacales

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Species 80
Genome length 154–164 kb
Candidate markers 244
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

3 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 244 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rbcL-accD LSC 2334 0.1282 0.90 76.8 yes View details
trnN-GUU-ndhF IRb 976 0.1521 0.96 80.5 yes View details
ndhH-trnN-GUU SSC 7409 0.0453 0.98 78.4 yes View details
ndhF-trnL-UAG SSC 1067 0.0207 0.99 74.4 yes View details
trnH-GUG-psbA LSC 339 0.0510 0.98 74.1 yes View details
trnE-UUC-trnT-GGU LSC 780 0.0231 1.00 73.8 yes View details
atpH-atpI LSC 1152 0.0098 1.00 73.1 yes View details
infA-rps8 LSC 180 0.0421 0.97 72.2 yes View details
trnT-UGU-trnL-UAA LSC 756 0.0170 1.00 69.5 yes View details
trnS-GCU-trnS-CGA LSC 745 0.0138 0.99 68.9 yes View details
rps12-psbB LSC 1182 0.0116 1.00 68.9 yes View details
trnK-UUU-trnQ-UUG LSC 3428 0.0140 0.99 68.7 yes View details
petA-psbJ LSC 1010 0.0151 1.00 68.7 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 65 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 TAGACCTAGCCGCTCTTGAA 238–575 1.000 89.8
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TAGACCTAGCCGCTCTTGAA 237–574 1.000 89.8
trnH-GUG-psbA_p3 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TAGACCTAGCCGCTCTTGAA 239–576 1.000 89.8
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CTAGACCTAGCCGCTCTTGA 239–576 1.000 88.4
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CTAGACCTAGCCGCTCTTGA 238–575 1.000 88.4
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG ACTTGTGTTGGATTGGCACT GCGGAGGCTTTTAAGGAACT 171–181 1.000 90.0
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG GACTTGTGTTGGATTGGCAC GCGGAGGCTTTTAAGGAACT 172–182 1.000 87.2
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG AGACTTGTGTTGGATTGGCA GCGGAGGCTTTTAAGGAACT 173–183 0.988 87.2
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG TGTGTTGGATTGGCACTACA GCGGAGGCTTTTAAGGAACT 168–178 1.000 85.4
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG TTGTGTTGGATTGGCACTACA GCGGAGGCTTTTAAGGAACT 169–179 1.000 82.1
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA ATTAGCAATCCGCCGCTTTA TGAATCAAACCGAAAGATCCCT 827–892 0.988 72.8
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA GCTCGTACAACGGATTAGCA TGAATCAAACCGAAAGATCCCT 840–905 0.988 72.4
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA ACGGAAAGAGAGGGATTCGA TGAATCAAACCGAAAGATCCCT 876–941 0.988 71.9
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA AGCTCGTACAACGGATTAGC TGAATCAAACCGAAAGATCCCT 841–906 0.988 71.4
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA TGGAAACGGAAAGAGAGGGA TGAATCAAACCGAAAGATCCCT 881–946 0.988 70.9
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1235–1273 1.000 87.6
atpH-atpI_p2 atpH-atpI GTTCCTTGACCAACTCCAGG TTTTTGCAACTTTAGCCGCG 1292–1330 1.000 87.0
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGT 1208–1246 1.000 87.0
atpH-atpI_p4 atpH-atpI CAGCAGTTCCTTGACCAACT TTTTTGCAACTTTAGCCGCG 1297–1335 0.950 85.5
atpH-atpI_p5 atpH-atpI CAGCAGTTCCTTGACCAACT TAGGTGAATCCATGGAGGGT 1270–1308 0.950 85.1
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGATCAACTCCCTTTCCCAG GAACCGATGACTTACGCCTT 545–1036 1.000 91.7
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGATCAACTCCCTTTCCCAG CCGATGACTTACGCCTTACC 542–1033 1.000 90.6
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGATCAACTCCCTTTCCCAG ACTCTACCGCTGACTGAGTT 514–1005 0.988 90.6
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TCCCTTTCCCAGTACCCTAC GAACCGATGACTTACGCCTT 537–1028 1.000 89.9
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGATCAACTCCCTTTCCCAG CGTTACTCTACCGCTGACTG 518–1009 0.988 89.9
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 796–832 0.988 89.9
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 788–824 0.975 89.9
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG AGTCCGTAGCGTCTACCAAT 802–838 1.000 89.0
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 828–864 0.975 88.5
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 820–856 0.963 88.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (80)

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

Species Accession Length (bp) Link
Lonicera acuminata PP697851.1 154611 View on NCBI ↗
Lonicera alpigena subsp. alpigena PP165069.1 155626 View on NCBI ↗
Lonicera alpigena subsp. formanekiana OQ784197.1 155993 View on NCBI ↗
Lonicera angustifolia PP697884.1 156084 View on NCBI ↗
Lonicera angustifolia var. myrtillus PP697894.1 156331 View on NCBI ↗
Lonicera bournei PP697917.1 154789 View on NCBI ↗
Lonicera caerulea PP697861.1 156111 View on NCBI ↗
Lonicera caerulea var. altaica PV026015.1 163889 View on NCBI ↗
Lonicera caerulea var. edulis OP345475.1 155142 View on NCBI ↗
Lonicera caerulea var. pallasii PV026016.1 164000 View on NCBI ↗
Lonicera californica OQ784208.1 155112 View on NCBI ↗
Lonicera cerviculata OQ784221.1 155236 View on NCBI ↗
Lonicera chrysantha NC_080500.1 154646 View on NCBI ↗
Lonicera ciliosa OQ784184.1 155242 View on NCBI ↗
Lonicera confusa NC_045045.1 155346 View on NCBI ↗
Lonicera conjugialis OQ784176.1 154441 View on NCBI ↗
Lonicera crassifolia NC_060585.1 154731 View on NCBI ↗
Lonicera cyanocarpa PP697858.1 154402 View on NCBI ↗
Lonicera discolor OQ784177.1 154881 View on NCBI ↗
Lonicera etrusca OQ784220.1 154601 View on NCBI ↗
Lonicera ferdinandi NC_040963.1 154513 View on NCBI ↗
Lonicera ferruginea OQ784219.1 154782 View on NCBI ↗
Lonicera fragrantissima NC_058578.1 154942 View on NCBI ↗
Lonicera fragrantissima var. lancifolia MG738669.1 154732 View on NCBI ↗
Lonicera fulvotomentosa NC_054349.1 155102 View on NCBI ↗
Lonicera harae NC_073106.1 154959 View on NCBI ↗
Lonicera hispida NC_040962.1 154553 View on NCBI ↗
Lonicera hypoglauca NC_054350.1 154581 View on NCBI ↗
Lonicera insularis NC_039634.1 155124 View on NCBI ↗
Lonicera interrupta OQ784196.1 154626 View on NCBI ↗
Lonicera involucrata OQ784212.1 154829 View on NCBI ↗
Lonicera japonica NC_026839.1 155078 View on NCBI ↗
Lonicera japonica var. chinensis OQ784225.1 155094 View on NCBI ↗
Lonicera kansuensis PP697895.1 155089 View on NCBI ↗
Lonicera lanceolata PP697875.1 154801 View on NCBI ↗
Lonicera leschenaultii OQ784178.1 154903 View on NCBI ↗
Lonicera ligustrina NC_067811.1 155330 View on NCBI ↗
Lonicera ligustrina var. pileata PP697893.1 155344 View on NCBI ↗
Lonicera litangensis PP697898.1 154937 View on NCBI ↗
Lonicera longiflora PP697926.1 154892 View on NCBI ↗
Lonicera maackii NC_039636.1 155318 View on NCBI ↗
Lonicera macrantha NC_082213.1 155169 View on NCBI ↗
Lonicera macranthoides NC_040959.1 154897 View on NCBI ↗
Lonicera micrantha PV026018.1 153985 View on NCBI ↗
Lonicera microphylla NC_072556.1 154945 View on NCBI ↗
Lonicera modesta var. lushanensis OM141002.1 154389 View on NCBI ↗
Lonicera nervosa NC_040961.1 154862 View on NCBI ↗
Lonicera nigra PP165070.1 155124 View on NCBI ↗
Lonicera oblata NC_064932.1 155481 View on NCBI ↗
Lonicera oblongifolia var. altissima OQ784210.1 154826 View on NCBI ↗
Lonicera olgae OQ784217.1 154417 View on NCBI ↗
Lonicera pampaninii OR567254.1 155360 View on NCBI ↗
Lonicera periclymenum NC_066027.1 155200 View on NCBI ↗
Lonicera persica OQ784222.1 155043 View on NCBI ↗
Lonicera praeflorens NC_039635.1 154892 View on NCBI ↗
Lonicera prostrata PP697870.1 154887 View on NCBI ↗
Lonicera reticulata PP697929.1 155135 View on NCBI ↗
Lonicera rupicola var. minuta PP697854.1 155561 View on NCBI ↗
Lonicera rupicola var. syringantha PP697855.1 155110 View on NCBI ↗
Lonicera ruprechtiana NC_056986.1 154611 View on NCBI ↗
Lonicera sachalinensis NC_039637.1 155123 View on NCBI ↗
Lonicera scabrida PP697857.1 155236 View on NCBI ↗
Lonicera semenovii PP697902.1 154459 View on NCBI ↗
Lonicera sempervirens PP697889.1 155440 View on NCBI ↗
Lonicera similis PP697853.1 155149 View on NCBI ↗
Lonicera spinosa PP697878.1 155269 View on NCBI ↗
Lonicera stephanocarpa NC_037954.1 155056 View on NCBI ↗
Lonicera subspicata OQ784203.1 154802 View on NCBI ↗
Lonicera subspicata var. denudata OQ784216.1 154740 View on NCBI ↗
Lonicera tangutica NC_071949.1 155709 View on NCBI ↗
Lonicera tatarica NC_059719.1 154677 View on NCBI ↗
Lonicera tatarica var. morrowii OQ784205.1 154871 View on NCBI ↗
Lonicera tatarinowii NC_080498.1 154725 View on NCBI ↗
Lonicera tragophylla NC_037953.1 155545 View on NCBI ↗
Lonicera trichosantha PP697940.1 154822 View on NCBI ↗
Lonicera tubuliflora PP697877.1 155703 View on NCBI ↗
Lonicera vesicaria NC_039638.1 155182 View on NCBI ↗
Lonicera webbiana PP697869.1 156192 View on NCBI ↗
Lonicera x heckrottii NC_058732.1 155437 View on NCBI ↗
Lonicera xylosteum PP165071.1 154636 View on NCBI ↗