Markers + reference

Gagea

4 species · Liliaceae · Liliales

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Species 4
Genome length 149–150 kb
Candidate markers 270
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 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ_UUG LSC 1014 0.0578 0.97 87.1 yes View details
trnS_GCU-trnG_UCC LSC 885 0.0503 0.97 86.2 yes View details
trnE_UUC-trnT_GGU LSC 612 0.0496 0.99 84.5 yes View details
trnT_UGU-trnL_UAA LSC 780 0.0543 0.96 88.5 yes View details
rbcL-accD LSC 789 0.0423 0.97 78.6 yes View details
psaJ-rpl33 LSC 540 0.0640 0.99 85.6 yes View details
ycf1 IRb 1044 0.0057 1.00 49.9 no View details
ndhF-rpl32 SSC 527 0.0737 0.96 81.3 yes View details
psaC-ndhE SSC 419 0.0534 0.98 78.6 yes View details
ycf1 SSC 5256 0.0248 1.00 56.6 yes View details
trnK-UUU-rps16 LSC 432 0.0494 0.98 86.2 yes View details
clpP-psbB LSC 446 0.0463 0.97 86.2 yes View details
psbK-psbI LSC 103 0.0599 0.98 80.7 yes View details
ndhG-ndhI SSC 345 0.0512 0.99 80.6 yes View details
trnL_UAA-trnF_GAA LSC 195 0.0538 0.96 80.5 yes View details
rps19-psbA LSC 103 0.0502 1.00 80.0 no View details
psbI-trnS_GCU LSC 141 0.0520 1.00 79.9 yes View details
trnW_CCA-trnP_UGG LSC 78 0.0641 1.00 78.7 yes View details
rpl22-rps19 LSC 69 0.0507 1.00 78.5 yes View details
petA-psbJ LSC 604 0.0453 1.00 77.8 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 90 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 AAAATGGCGCTCAACCTACA 529–565 1.000 87.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAATGGCGCTCAACCTACA 528–564 1.000 87.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TGAAAATGGCGCTCAACCTA 531–567 1.000 86.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGAAAATGGCGCTCAACCTA 530–566 1.000 86.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAATGGCGCTCAACC 532–568 1.000 85.9
rps16-trnQ_UUG_p1 rps16-trnQ_UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 992–1123 1.000 90.0
rps16-trnQ_UUG_p2 rps16-trnQ_UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1003–1134 1.000 89.4
rps16-trnQ_UUG_p3 rps16-trnQ_UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 996–1127 1.000 88.9
rps16-trnQ_UUG_p4 rps16-trnQ_UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1007–1138 1.000 88.3
rps16-trnQ_UUG_p5 rps16-trnQ_UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 998–1129 1.000 87.1
psbK-psbI_p1 psbK-psbI GCAGGCTGCTGTAAGTTTTC ACGAAGAGTTTGAGAGTAAGCA 150–156 1.000 66.4
psbK-psbI_p2 psbK-psbI AGGCTGCTGTAAGTTTTCGA ACGAAGAGTTTGAGAGTAAGCA 148–154 1.000 64.8
psbK-psbI_p3 psbK-psbI CAGGCTGCTGTAAGTTTTCG ACGAAGAGTTTGAGAGTAAGCA 149–155 1.000 64.3
psbK-psbI_p4 psbK-psbI GCAGGCTGCTGTAAGTTTTC AACGAAGAGTTTGAGAGTAAGCA 151–157 1.000 62.6
psbK-psbI_p5 psbK-psbI GCAGGCTGCTGTAAGTTTTC ACGAAGAGTTTGAGAGTAAGCAT 150–156 1.000 61.9
psbI-trnS_GCU_p1 psbI-trnS_GCU GCAATCCTGGACGTGAAGAA GGGTTCGAATCCCTCTCTCT 176–187 1.000 86.8
psbI-trnS_GCU_p2 psbI-trnS_GCU GCAATCCTGGACGTGAAGAA TTCGAATCCCTCTCTCTCCG 173–184 1.000 86.1
psbI-trnS_GCU_p3 psbI-trnS_GCU GCAATCCTGGACGTGAAGAA GGTTCGAATCCCTCTCTCTC 175–186 1.000 79.3
psbI-trnS_GCU_p4 psbI-trnS_GCU GCAATCCTGGACGTGAAGAA GTTCGAATCCCTCTCTCTCC 174–185 1.000 79.3
psbI-trnS_GCU_p5 psbI-trnS_GCU GCAATCCTGGACGTGAAGAA TCGAATCCCTCTCTCTCCG 172–183 1.000 77.5
trnS_GCU-trnG_UCC_p1 trnS_GCU-trnG_UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 938–994 1.000 62.1
trnS_GCU-trnG_UCC_p2 trnS_GCU-trnG_UCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 941–997 1.000 61.0
trnS_GCU-trnG_UCC_p3 trnS_GCU-trnG_UCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 940–996 1.000 61.0
trnS_GCU-trnG_UCC_p4 trnS_GCU-trnG_UCC ATTAGCAATCCGCCGCTTTA AGGGGTTAATAGAACGAATCACA 951–1007 1.000 60.8
trnS_GCU-trnG_UCC_p5 trnS_GCU-trnG_UCC ATTAGCAATCCGCCGCTTTA GGGGTTAATAGAACGAATCACAC 950–1006 1.000 60.5
trnE_UUC-trnT_GGU_p1 trnE_UUC-trnT_GGU CCCAGCAAGATGTATGGCAT GAACCGATGACTTACGCCTT 1169–1249 1.000 87.3
trnE_UUC-trnT_GGU_p2 trnE_UUC-trnT_GGU GGATCCTAGTTCGGGACTGA GAACCGATGACTTACGCCTT 1251–1331 1.000 86.3
trnE_UUC-trnT_GGU_p3 trnE_UUC-trnT_GGU CCCAGCAAGATGTATGGCAT TGGGTCAGATCCACTTACGT 1401–1492 1.000 86.3
trnE_UUC-trnT_GGU_p4 trnE_UUC-trnT_GGU CCCAGCAAGATGTATGGCAT CCATGGCGTTACTCTACCAC 1148–1228 0.750 74.7
trnE_UUC-trnT_GGU_p5 trnE_UUC-trnT_GGU CTTGCTCCCTGTCCCATTTT GAACCGATGACTTACGCCTT 1307 0.250 49.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Gagea khassanovii PQ351603.1 149155 View on NCBI ↗
Gagea lutea PP336752.1 149756 View on NCBI ↗
Gagea tibetica NC_058295.1 150379 View on NCBI ↗
Gagea triflora MT261157.1 150345 View on NCBI ↗