Markers + reference

Erythronium

11 species · Liliaceae · Liliales

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Species 11
Genome length 151–152 kb
Candidate markers 264
Primer pairs 120

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 866 0.0219 0.96 68.1 yes View details
trnS-GCU-trnG-UCC LSC 705 0.0216 0.99 80.4 yes View details
trnE-UUC-trnT-GGU LSC 850 0.0223 0.82 61.9 yes View details
accD-psaI LSC 811 0.0211 0.99 67.9 yes View details
petA-psbJ LSC 659 0.0208 0.98 58.7 yes View details
psbE-petL LSC 1153 0.0223 0.98 74.5 yes View details
trnP-UGG-psaJ LSC 405 0.0244 0.98 67.4 yes View details
psaJ-rpl33 LSC 608 0.0303 0.91 71.3 yes View details
rpoA LSC 1020 0.0061 1.00 37.0 yes View details
trnN-GUU-ndhF IRb 1870 0.0076 0.84 40.2 yes View details
ndhF-rpl32 SSC 719 0.0233 0.97 66.4 yes View details
rpl32-trnL-UAG SSC 680 0.0238 0.95 72.0 yes View details
rps15-ycf1 SSC 416 0.0255 0.97 60.9 yes View details
ycf1 SSC 5388 0.0145 0.99 51.6 yes View details
pafII-cemA LSC 554 0.0200 0.94 72.0 yes View details
rps18-rpl20 LSC 268 0.0365 0.94 70.8 yes View details
ndhC-trnV-UAC LSC 983 0.0176 0.96 70.2 yes View details
rpoB-trnC-GCA LSC 880 0.0174 0.97 68.7 yes View details
trnT-UGU-trnL-UAA LSC 758 0.0167 0.97 65.4 yes View details
rbcL-accD LSC 903 0.0151 0.96 64.9 yes View details
trnS-GGA-rps4 LSC 305 0.0172 0.99 64.8 yes View details
psbM-trnD-GUC LSC 500 0.0111 0.95 63.1 yes View details
ndhE-ndhG SSC 191 0.0377 0.97 62.7 yes View details
rpl22-rps19 LSC 59 0.0356 0.98 61.8 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 120 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 909–939 1.000 86.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 920–950 1.000 85.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 913–943 1.000 85.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 924–954 1.000 84.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CGGTAAGGCAATGGGTTTTG 942–972 1.000 84.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC AAGGGATAGCGGAGAGAGAG ACGAATCACACTTTTACCACT 836–864 1.000 57.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC TAGCGGAGAGAGAGGGATTC ACGAATCACACTTTTACCACT 830–858 1.000 57.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA ACGAATCACACTTTTACCACT 827–855 1.000 57.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TAGCGGAGAGAGAGGGATTC AGAACGAATCACACTTTTACCAC 833–861 1.000 56.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TAGCGGAGAGAGAGGGATTC GAACGAATCACACTTTTACCACT 832–860 1.000 56.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCGTCAAGCCCTGATTAATGA GCGACACCCAGATTTGAACT 1001–1046 1.000 75.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCCGTCAAGCCCTGATTAATG GCGACACCCAGATTTGAACT 1002–1047 1.000 75.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCGTCAAGCCCTGATTAATGA TAAAGGATTTGCAGTCCCCC 976–1021 1.000 74.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCCGTCAAGCCCTGATTAATG TAAAGGATTTGCAGTCCCCC 977–1022 1.000 74.8
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCGTCAAGCCCTGATTAATGA CCTTACCACTTGGCCATGTC 955–1000 1.000 74.8
psbM-trnD-GUC_p1 psbM-trnD-GUC TGCGAGAATATTGACTTCCA CCTCGCTGGGATTGTAGTTC 572–602 1.000 58.5
psbM-trnD-GUC_p2 psbM-trnD-GUC TGCGAGAATATTGACTTCCA TGTATGCCATAACCTCGCTG 584–614 1.000 57.0
psbM-trnD-GUC_p3 psbM-trnD-GUC TGCGAGAATATTGACTTCCA CATAACCTCGCTGGGATTGT 577–607 1.000 56.3
psbM-trnD-GUC_p4 psbM-trnD-GUC TGCGAGAATATTGACTTCCA CCATAACCTCGCTGGGATTG 578–608 1.000 55.8
psbM-trnD-GUC_p5 psbM-trnD-GUC TGCGAGAATATTGACTTCCAT CCTCGCTGGGATTGTAGTTC 572–602 1.000 55.5
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCATCGACCCAGGAAGAATT GAACCGATGACTTACGCCTT 918–1169 1.000 88.0
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CTTGCTTCCTGTCCCACTTT GAACCGATGACTTACGCCTT 1425–1682 1.000 87.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GAACTACAATCCCAGCGAGG GAACCGATGACTTACGCCTT 1297–1554 1.000 87.3
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AATGGAGCGGCGAATTTTTG GAACCGATGACTTACGCCTT 1111–1139 0.182 50.1
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CAATGGAGCGGCGAATTTTT GAACCGATGACTTACGCCTT 1112–1140 0.182 50.1
trnS-GGA-rps4_p1 trnS-GGA-rps4 AGGCTTTTGTTTACCGAGGG ATTATTCCCGTCAGACTTGA 353–365 1.000 51.8
trnS-GGA-rps4_p2 trnS-GGA-rps4 CACTCGGTTTCTGGCCAATA ATTATTCCCGTCAGACTTGA 433–445 1.000 50.5
trnS-GGA-rps4_p3 trnS-GGA-rps4 GGCTTTTGTTTACCGAGGGT ATTATTCCCGTCAGACTTGA 352–364 1.000 49.5
trnS-GGA-rps4_p4 trnS-GGA-rps4 TATGAAGGAGAGATGGCCGA ATTATTCCCGTCAGACTTGA 406–418 1.000 48.7
trnS-GGA-rps4_p5 trnS-GGA-rps4 AGGCTTTTGTTTACCGAGGG AGTCGTAGAATATTATTCCCGTCA 364–376 1.000 46.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Erythronium albidum PX122074.1 151599 View on NCBI ↗
Erythronium americanum PX122075.1 151114 View on NCBI ↗
Erythronium californicum PX122076.1 150715 View on NCBI ↗
Erythronium caucasicum PX122077.1 151312 View on NCBI ↗
Erythronium citrinum PX122078.1 150695 View on NCBI ↗
Erythronium dens-canis PX122079.1 151333 View on NCBI ↗
Erythronium grandiflorum PX122080.1 150647 View on NCBI ↗
Erythronium japonicum PX122081.1 151827 View on NCBI ↗
Erythronium multiscapideum PX122082.1 150727 View on NCBI ↗
Erythronium revolutum PX122083.1 150651 View on NCBI ↗
Erythronium tuolumnense PX122084.1 150761 View on NCBI ↗