Markers + reference

Leucojum

2 species · Amaryllidaceae · Asparagales

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Species 2
Genome length 157–157 kb
Candidate markers 271
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 585 0.0363 0.99 70.1 yes View details
rps16-trnQ-UUG LSC 1375 0.0284 0.85 64.9 yes View details
trnS-GCU-trnG-GCC LSC 1284 0.0419 0.82 73.6 yes View details
ndhC-trnV-UAC LSC 1570 0.0157 0.77 55.8 yes View details
ycf4-cemA LSC 798 0.0296 0.97 64.3 yes View details
petA-psbJ LSC 1160 0.0347 0.55 65.5 yes View details
ndhF SSC 2229 0.0148 1.00 51.0 yes View details
ndhF-rpl32 SSC 924 0.0189 0.97 65.5 yes View details
rpl32-trnL-UAG SSC 789 0.0280 1.00 60.9 yes View details
ycf1 SSC 5388 0.0178 1.00 48.5 yes View details
trnW-CCA-trnP-UGG LSC 170 0.0414 0.99 73.6 yes View details
atpF-atpH LSC 495 0.0264 1.00 72.0 yes View details
psbC-trnS-UGA LSC 127 0.0630 1.00 71.2 yes View details
rps19-psbA LSC 128 0.0703 1.00 69.7 no View details
atpB-rbcL LSC 843 0.0143 1.00 67.2 yes View details
ndhA SSC 2219 0.0141 0.99 66.2 yes View details
trnD-GUC-trnY-GUA LSC 371 0.0291 0.93 66.1 yes View details
rpl33-rps18 LSC 182 0.0301 0.91 65.8 yes View details
psbA-trnK-UUU LSC 239 0.0377 1.00 64.7 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU GCTTGTACTTTCGCGTCTCT GTTTGGGGAGGGGTCTTTTT 365 1.000 78.8
psbA-trnK-UUU_p2 psbA-trnK-UUU CCCCACAGGCTTGTACTTTC GTTTGGGGAGGGGTCTTTTT 373 1.000 77.4
psbA-trnK-UUU_p3 psbA-trnK-UUU GCTTGTACTTTCGCGTCTCT TTTGGGGAGGGGTCTTTTTC 364 1.000 76.4
psbA-trnK-UUU_p4 psbA-trnK-UUU GCTTGTACTTTCGCGTCTCT AAAATGCAAGCACGGTTTGG 379 1.000 76.1
psbA-trnK-UUU_p5 psbA-trnK-UUU ATCCAGTTACAGAAGCGACC GTTTGGGGAGGGGTCTTTTT 391 1.000 75.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCAGAATTATTTAAAGAAAGAGCTTCG 644–649 1.000 43.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCAGAATTATTTAAAGAAAGAGCTTCG 643–648 1.000 43.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ACTGTTCATGATATTTTAAGGAAAGCA 668–673 1.000 43.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ACTGTTCATGATATTTTAAGGAAAGCA 667–672 1.000 43.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGTTCATGATATTTTAAGGAAAGCAGA 665–670 1.000 43.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1262–1448 1.000 84.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1273–1459 1.000 83.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCGAATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1283–1469 1.000 83.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1266–1452 1.000 79.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 1274–1460 1.000 79.2
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CTCGTCCAACGGATTAGCAA CGAACGAATCACACTTTTACCA 1229–1373 1.000 64.9
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AACTCGTCCAACGGATTAGC CGAACGAATCACACTTTTACCA 1231–1375 1.000 64.9
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA CGAACGAATCACACTTTTACCA 1217–1361 1.000 64.7
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CTCGTCCAACGGATTAGCAA TCGAACGAATCACACTTTTACC 1230–1374 1.000 62.8
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AACTCGTCCAACGGATTAGC TCGAACGAATCACACTTTTACC 1232–1376 1.000 62.8
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG ATTTATGGACTGGTCGTGGC 616–618 1.000 80.7
atpF-atpH_p2 atpF-atpH CAGTGGCCTAAGGAAACGAA ATTTATGGACTGGTCGTGGC 588–590 1.000 80.3
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG TCGTGGCATTAGCGCTTTTA 603–605 1.000 78.9
atpF-atpH_p4 atpF-atpH CAGTGGCCTAAGGAAACGAA TCGTGGCATTAGCGCTTTTA 575–577 1.000 78.5
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG CGTGGCATTAGCGCTTTTAT 602–604 1.000 75.0
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GTGCTCTGACCGATTGAACT GGGGACGGACTGTAAATTCG 434–460 1.000 82.3
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA GTGCTCTGACCGATTGAACT GACATGTCTACGCTGGTTCA 409–435 1.000 82.3
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA GGGGACGGACTGTAAATTCG 491–517 1.000 82.2
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA GACATGTCTACGCTGGTTCA 466–492 1.000 82.2
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA GGGACGGACTGTAAATTCGT 490–516 1.000 82.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Leucojum aestivum PP853217.1 157356 View on NCBI ↗
Leucojum vernum OR884996.1 156693 View on NCBI ↗