Markers + reference

Fritillaria

33 species · Liliaceae · Liliales

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Species 33
Genome length 151–152 kb
Candidate markers 268
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 731 0.0189 0.99 81.0 yes View details
rpoB-trnC-GCA LSC 671 0.0170 0.99 72.0 yes View details
psbM-trnD-GUC LSC 1058 0.0153 0.95 66.1 yes View details
trnD-GUC-trnY-GUA LSC 304 0.0231 0.99 70.2 yes View details
trnE-UUC-trnT-GGU LSC 675 0.0206 0.99 75.2 yes View details
trnT-GGU-psbD LSC 1109 0.0138 0.99 63.9 yes View details
trnT-UGU-trnL-UAA LSC 772 0.0212 1.00 73.6 yes View details
ycf4-cemA LSC 734 0.0225 1.00 63.8 yes View details
ycf1 IRb 1263 0.0049 1.00 53.9 no View details
rpl32-trnL-UAG SSC 743 0.0232 0.99 74.3 yes View details
ycf1 SSC 5544 0.0126 1.00 56.0 yes View details
rpl22-rps19 LSC 108 0.0409 0.96 70.6 yes View details
psbE-petL LSC 1216 0.0105 0.97 70.2 yes View details
trnH-GUG-psbA IRa 247 0.0174 1.00 69.7 no View details
atpH-atpI LSC 886 0.0137 1.00 67.6 yes View details
petA-psbJ LSC 804 0.0154 1.00 66.5 yes View details
ndhC-trnV-UAC LSC 737 0.0125 0.99 65.7 yes View details
ndhG-ndhI SSC 394 0.0139 0.99 64.2 yes View details
rpl36-rps8 LSC 459 0.0159 1.00 63.2 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCTCAACCCACAGTAACTGT 746–847 1.000 88.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAACCCACAGTAACTGT 745–846 1.000 88.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CTTGAAAATGGCGCTCAACC 758–859 1.000 88.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CCTTGAAAATGGCGCTCAAC 758–859 1.000 88.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAATGGCGCTCAACC 757–858 1.000 88.3
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 895–988 0.970 83.6
atpH-atpI_p2 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 896–989 0.970 82.5
atpH-atpI_p3 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTTGCAACTTTAGCCGCG 910–1003 0.970 82.1
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGT 868–961 0.909 80.4
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA TAGGTGAATCCATGGAGGGT 869–962 0.909 79.2
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AAGCCCCGATTAATGAACCC GCGACACCCAGATTTGAACT 811–834 1.000 87.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AAGCCCCGATTAATGAACCC CCTTACCACTTGGCCATGTC 765–788 1.000 87.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AAGCCCCGATTAATGAACCC TTTGTCAATCAGGCGACACC 823–846 1.000 84.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCCCGATTAATGAACCCACA GCGACACCCAGATTTGAACT 808–831 1.000 84.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AAGCCCCGATTAATGAACCC TAAAGGATTTGCAGTCCCCC 786–809 0.939 84.0
psbM-trnD-GUC_p1 psbM-trnD-GUC TGCGAGAATATTAACTTCCA CCTCGCTGGGATTGTAGTTC 1101–1160 1.000 51.7
psbM-trnD-GUC_p2 psbM-trnD-GUC TGCGAGAATATTAACTTCCA TACACCTCGCTGGGATTGTA 1105–1164 1.000 51.7
psbM-trnD-GUC_p3 psbM-trnD-GUC ATGCGAGAATATTAACTTCCA CCTCGCTGGGATTGTAGTTC 1102–1161 1.000 51.7
psbM-trnD-GUC_p4 psbM-trnD-GUC TGCGAGAATATTAACTTCCAT CCTCGCTGGGATTGTAGTTC 1101–1160 1.000 51.7
psbM-trnD-GUC_p5 psbM-trnD-GUC TGCGAGAATATTAACTTCCA CATACACCTCGCTGGGATTG 1107–1166 1.000 51.7
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA TGGCAATATGTCTACGCTGG 415–458 1.000 89.5
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA GGCAATATGTCTACGCTGGT 414–457 1.000 89.5
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA CGGACTGTAAATTCGTTGGC 431–474 1.000 87.3
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA ATCGGATCCTAGTTCGGGAC TGGCAATATGTCTACGCTGG 418–461 1.000 87.0
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CATCGGATCCTAGTTCGGGA TGGCAATATGTCTACGCTGG 419–462 1.000 87.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 672–768 1.000 90.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 670–766 1.000 90.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 726–822 1.000 90.7
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 651–747 1.000 90.3
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 649–745 1.000 90.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (33)

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

Species Accession Length (bp) Link
Fritillaria anhuiensis NC_045861.1 152196 View on NCBI ↗
Fritillaria baisunensis OR935787.1 152027 View on NCBI ↗
Fritillaria bucharica OR935789.1 151980 View on NCBI ↗
Fritillaria cirrhosa NC_024728.1 151991 View on NCBI ↗
Fritillaria cirrhosa var. ecirrhosa PX427817.1 152065 View on NCBI ↗
Fritillaria crassicaulis NC_045860.1 151852 View on NCBI ↗
Fritillaria dajinensis NC_044632.1 151991 View on NCBI ↗
Fritillaria davidii NC_045895.1 152044 View on NCBI ↗
Fritillaria delavayi NC_046473.1 151948 View on NCBI ↗
Fritillaria eduardii NC_037038.1 152224 View on NCBI ↗
Fritillaria ferganensis OR935792.1 151725 View on NCBI ↗
Fritillaria fusca NC_060547.1 151739 View on NCBI ↗
Fritillaria gibbosa OR935794.1 152032 View on NCBI ↗
Fritillaria meleagroides NC_037040.1 151846 View on NCBI ↗
Fritillaria mellea PX427828.1 151071 View on NCBI ↗
Fritillaria monantha NC_046472.1 152158 View on NCBI ↗
Fritillaria olgae OR935797.1 151916 View on NCBI ↗
Fritillaria omeiensis MN810995.1 152019 View on NCBI ↗
Fritillaria persica NC_037039.1 151803 View on NCBI ↗
Fritillaria przewalskii NC_044636.1 151983 View on NCBI ↗
Fritillaria rugillosa OR935798.1 151933 View on NCBI ↗
Fritillaria sewerzowii OR935802.1 151756 View on NCBI ↗
Fritillaria sichuanica NC_044628.1 151958 View on NCBI ↗
Fritillaria sinica NC_044631.1 152064 View on NCBI ↗
Fritillaria stenanthera OR935804.1 152344 View on NCBI ↗
Fritillaria taipaiensis NC_023247.1 151693 View on NCBI ↗
Fritillaria thunbergii NC_034368.1 152155 View on NCBI ↗
Fritillaria unibracteata NC_044629.1 151058 View on NCBI ↗
Fritillaria unibracteata var. longinectarea PP663674.1 151014 View on NCBI ↗
Fritillaria unibracteata var. maculata PX427839.1 151073 View on NCBI ↗
Fritillaria unibracteata var. wabuensis KF769142.1 151009 View on NCBI ↗
Fritillaria usuriensis NC_034369.1 151524 View on NCBI ↗
Fritillaria yuzhongensis NC_044630.1 151645 View on NCBI ↗