Markers + reference

Lilium

66 species · Liliaceae · Liliales

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Species 66
Genome length 152–153 kb
Candidate markers 270
Primer pairs 115

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 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 749 0.0181 0.97 72.3 yes View details
rps16-trnQ-UUG LSC 625 0.0174 0.99 66.5 yes View details
trnS-GCU-trnG-UCC LSC 680 0.0201 0.95 66.8 yes View details
trnT-UGU-trnL-UAA LSC 762 0.0154 0.99 77.3 yes View details
trnP-UGG-psaJ LSC 340 0.0150 0.98 58.9 yes View details
rpoA LSC 1008 0.0068 1.00 46.2 yes View details
rps19 LSC 279 0.0066 1.00 32.7 yes View details
rrn5-trnR-ACG IRb 250 0.0068 1.00 51.7 yes View details
ycf1 IRb 1263 0.0036 1.00 44.5 no View details
rpl32-trnL-UAG SSC 711 0.0205 0.88 60.4 yes View details
rps15-ycf1 SSC 404 0.0286 0.97 65.1 yes View details
ycf1 SSC 5577 0.0080 1.00 53.1 yes View details
trnR-ACG-rrn5S IRa 250 0.0068 1.00 51.7 yes View details
psbZ-trnG-GCC LSC 287 0.0199 1.00 65.9 yes View details
atpH-atpI LSC 885 0.0100 0.97 63.8 yes View details
psbC-trnS-UGA LSC 137 0.0358 1.00 63.6 yes View details
psbM-trnD-GUC LSC 1182 0.0097 0.98 63.0 yes View details
ndhF-rpl32 SSC 407 0.0167 1.00 62.9 yes View details
trnF-GAA-ndhJ LSC 770 0.0136 0.99 62.1 yes View details
rps2-rpoC2 LSC 232 0.0234 1.00 61.6 yes View details
ccsA-ndhD SSC 174 0.0330 0.98 61.6 yes View details
ycf3-trnS-GGA LSC 572 0.0113 0.99 61.3 yes View details
trnT-GGU-psbD LSC 902 0.0143 0.99 61.1 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 115 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TTTCAAGGACTCCCAAGCAC TATTTTGGCGGGATGGGATC 2902–2969 0.970 87.4
trnK-UUU_p2 trnK-UUU AGGACTCCCAAGCACACATA TATTTTGGCGGGATGGGATC 2897–2964 0.970 84.9
trnK-UUU_p3 trnK-UUU TTTCAAGGACTCCCAAGCAC TTATTTTGGCGGGATGGGAT 2903–2970 0.970 83.6
trnK-UUU_p4 trnK-UUU TTTCAAGGACTCCCAAGCAC GGCGGGATGGGATCAATTTT 2909–2963 0.455 59.0
trnK-UUU_p5 trnK-UUU GTGCTTTCGCGTCTCTCTAA GGCGGGATGGGATCAATTTT 2963–3000 0.303 52.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCTCAACCCACAGTAACTGT 516–882 1.000 88.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAACCCACAGTAACTGT 515–881 1.000 88.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CTTGAAAATGGCGCTCAACC 528–894 1.000 88.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CCTTGAAAATGGCGCTCAAC 528–894 1.000 88.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAATGGCGCTCAACC 527–893 1.000 88.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 364–865 1.000 89.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 375–876 1.000 88.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 368–869 1.000 88.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGCGGATGTAAGAATCCACA GAGGTTCGAATCCTTCCGTC 400–901 1.000 87.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGGCGGATGTAAGAATCCAC GAGGTTCGAATCCTTCCGTC 401–902 1.000 87.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA TGTCGGAAACTGAAAGACCC 723–840 1.000 89.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA CGGAAACTGAAAGACCCCTT 720–837 1.000 89.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GAGGGATAGCGGAGAGAGAG TGTCGGAAACTGAAAGACCC 782–899 1.000 88.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GAGGGATAGCGGAGAGAGAG CGGAAACTGAAAGACCCCTT 779–896 1.000 88.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GATGAGGGATAGCGGAGAGA TGTCGGAAACTGAAAGACCC 785–902 1.000 88.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 629–995 1.000 86.5
atpH-atpI_p2 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 630–996 1.000 85.3
atpH-atpI_p3 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTTGCAACTTTAGCCGCG 644–1010 1.000 84.9
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGT 602–968 0.970 84.2
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA TAGGTGAATCCATGGAGGGT 603–969 0.970 83.0
rps2-rpoC2_p1 rps2-rpoC2 ACTCCCGCTTCCATCATTTC TGGGACATCACAACAACCAT 312–340 0.985 85.7
rps2-rpoC2_p2 rps2-rpoC2 ACTCCCGCTTCCATCATTTC CACAACAACCATTTACGCGA 304–332 0.955 84.5
rps2-rpoC2_p3 rps2-rpoC2 ACTCCCGCTTCCATCATTTC TCACAACAACCATTTACGCG 305–333 0.955 84.5
rps2-rpoC2_p4 rps2-rpoC2 TTTGCAGAGATGTAAGGGGC CACAACAACCATTTACGCGA 364–392 0.955 83.8
rps2-rpoC2_p5 rps2-rpoC2 TTTGCAGAGATGTAAGGGGC TCACAACAACCATTTACGCG 365–393 0.955 83.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (66)

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

Species Accession Length (bp) Link
Lilium amabile NC_035988.1 152567 View on NCBI ↗
Lilium amoenum NC_053564.1 152280 View on NCBI ↗
Lilium anhuiense NC_060549.1 152652 View on NCBI ↗
Lilium apertum NC_052786.1 152042 View on NCBI ↗
Lilium bakerianum NC_035592.1 151655 View on NCBI ↗
Lilium basilissum PX427841.1 151973 View on NCBI ↗
Lilium brownii NC_035588.1 152677 View on NCBI ↗
Lilium brownii var. viridulum NC_050268.1 152665 View on NCBI ↗
Lilium bulbiferum NC_037517.1 152686 View on NCBI ↗
Lilium bulbiferum subsp. bulbiferum PP336772.1 152646 View on NCBI ↗
Lilium callosum NC_035989.1 152626 View on NCBI ↗
Lilium candidum NC_042399.1 152101 View on NCBI ↗
Lilium cernuum NC_034840.1 152604 View on NCBI ↗
Lilium concolor NC_058994.1 152625 View on NCBI ↗
Lilium concolor var. partheneion OP784245.1 152646 View on NCBI ↗
Lilium concolor var. pulchellum MZ751064.1 152626 View on NCBI ↗
Lilium davidii NC_060550.1 152126 View on NCBI ↗
Lilium davidii var. unicolor MK954110.1 152659 View on NCBI ↗
Lilium distichum NC_029937.1 152598 View on NCBI ↗
Lilium duchartrei NC_035591.1 152287 View on NCBI ↗
Lilium fargesii NC_033908.1 153235 View on NCBI ↗
Lilium formosanum NC_042398.1 152653 View on NCBI ↗
Lilium gongshanense NC_052787.1 151974 View on NCBI ↗
Lilium hansonii NC_027674.1 152655 View on NCBI ↗
Lilium henryi NC_035570.1 153119 View on NCBI ↗
Lilium japonicum NC_049018.1 152613 View on NCBI ↗
Lilium jinfushanense PP130591.1 152145 View on NCBI ↗
Lilium lancifolium NC_035589.1 152574 View on NCBI ↗
Lilium lankongense NC_062580.1 152562 View on NCBI ↗
Lilium leichtlinii PQ663720.1 152053 View on NCBI ↗
Lilium leichtlinii subsp. maximowiczii OP756529.1 152049 View on NCBI ↗
Lilium leucanthum NC_035590.1 152935 View on NCBI ↗
Lilium liangiae OR353690.1 152548 View on NCBI ↗
Lilium lijiangense PP155506.1 152141 View on NCBI ↗
Lilium longiflorum NC_063560.1 152666 View on NCBI ↗
Lilium lophophorum PP130590.1 151636 View on NCBI ↗
Lilium martagon PP336773.1 152598 View on NCBI ↗
Lilium martagon var. pilosiusculum NC_039162.1 152816 View on NCBI ↗
Lilium matangense MN745201.1 152402 View on NCBI ↗
Lilium medogense OR797709.1 152356 View on NCBI ↗
Lilium meleagrinum NC_052788.1 152197 View on NCBI ↗
Lilium nanum PQ824868.1 152848 View on NCBI ↗
Lilium nepalense NC_052789.1 152316 View on NCBI ↗
Lilium papilliferum PX831860.1 152368 View on NCBI ↗
Lilium paradoxum PP073960.1 151814 View on NCBI ↗
Lilium pardalinum MH029495.1 151969 View on NCBI ↗
Lilium pardanthinum NC_038193.1 152718 View on NCBI ↗
Lilium pensylvanicum NC_043876.1 152063 View on NCBI ↗
Lilium philadelphicum NC_035990.1 152175 View on NCBI ↗
Lilium primulinum var. ochraceum KY748298.1 152306 View on NCBI ↗
Lilium pumilum NC_050269.1 152573 View on NCBI ↗
Lilium regale NC_052790.1 153082 View on NCBI ↗
Lilium rosthornii NC_054295.1 152956 View on NCBI ↗
Lilium saccatum OR353687.1 151839 View on NCBI ↗
Lilium saluenense OR353700.1 152046 View on NCBI ↗
Lilium sargentiae NC_052791.1 153129 View on NCBI ↗
Lilium sealyi NC_060548.1 152024 View on NCBI ↗
Lilium speciosum var. gloriosoides NC_060551.1 152597 View on NCBI ↗
Lilium sulphureum NC_052792.1 153107 View on NCBI ↗
Lilium superbum NC_026787.1 152069 View on NCBI ↗
Lilium taliense NC_034370.1 153055 View on NCBI ↗
Lilium tsingtauense NC_027675.1 152710 View on NCBI ↗
Lilium wardii OP784244.1 152268 View on NCBI ↗
Lilium washingtonianum NC_037699.1 151967 View on NCBI ↗
Lilium xanthellum MN745202.1 152307 View on NCBI ↗
Lilium yapingense OR353695.1 152035 View on NCBI ↗