Markers + reference

Notholirion

4 species · Liliaceae · Liliales

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Species 4
Genome length 153–153 kb
Candidate markers 263
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 732 0.0146 0.99 59.8 yes View details
trnC-GCA-petN LSC 548 0.0040 1.00 42.6 yes View details
accD-psaI LSC 798 0.0100 1.00 56.5 yes View details
ycf4-cemA LSC 944 0.0081 1.00 56.4 yes View details
rps8 LSC 399 0.0025 1.00 28.5 yes View details
rpl16 LSC 1408 0.0039 1.00 40.9 yes View details
rps19 IRb 279 0.0054 1.00 31.9 yes View details
ndhD SSC 1506 0.0030 1.00 35.1 yes View details
psaC-ndhE SSC 395 0.0190 1.00 45.6 yes View details
ndhG-ndhI SSC 402 0.0266 1.00 73.9 yes View details
rps19 IRa 138 0.0145 0.35 30.1 no View details
rpl22-rps19 LSC 222 0.0417 0.99 71.0 yes View details
rpl20-rps12 LSC 772 0.0035 1.00 61.1 yes View details
rpoB-trnC-GCA LSC 661 0.0086 1.00 58.2 yes View details
rps12-clpP LSC 153 0.0142 1.00 58.1 yes View details
psaB LSC 2205 0.0009 1.00 57.9 yes View details
psbK-psbI LSC 136 0.0075 0.98 57.5 yes View details
petA-psbJ LSC 811 0.0059 0.86 56.2 yes View details
psbM-trnD-GUC LSC 1182 0.0051 0.99 55.9 yes View details
psaA-ycf3 LSC 589 0.0088 1.00 55.8 yes View details
matK LSC 1542 0.0039 1.00 55.2 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK_p1 matK TCAATCATTTGGAAATTGGATCA CCTGTTCGGACCATATTGCA 1738–1743 1.000 40.6
matK_p2 matK TCAATCATTTGGAAATTGGATCA AAGAAATGCCCCCTGTCTTG 1683–1688 1.000 40.6
matK_p3 matK TCAATCATTTGGAAATTGGATCA CAAGAAATGCCCCCTGTCTT 1684–1689 1.000 40.6
matK_p4 matK TCAATCATTTGGAAATTGGATCA ATAACCCAAGAAATGCCCCC 1690–1695 1.000 40.6
matK_p5 matK TGTCTATCAATCATTTGGAAATTGGA CCTGTTCGGACCATATTGCA 1744–1749 1.000 40.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGGAAGACAGAATTATTTAAAGAAGGA 785–805 1.000 44.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGAAGACAGAATTATTTAAAGAAGGA 784–804 1.000 44.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGAAGACAGAATTATTTAAAGAAGGA 784–804 1.000 44.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGAAGACAGAATTATTTAAAGAAGGA 783–803 1.000 44.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGAAGACAGAATTATTTAAAGAAGG 784–804 1.000 44.1
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGATTGCGTCCTGGATCATT 253–261 1.000 82.4
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCACGTCCAGGATTGC 266–274 1.000 81.0
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT GGATTGCGTCCTGGATCATT 250–258 1.000 80.5
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT GGATTGCGTCCTGGATCATT 251–259 1.000 80.4
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT GGATTGCGTCCTGGATCATT 252–260 1.000 80.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GCCAAGCCCCGATTAATGAA TTAGGCGACACCCAGATTTG 829–843 1.000 75.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GCCAAGCCCCGATTAATGAA TTGTCAATTAGGCGACACCC 836–850 1.000 74.9
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GCCAAGCCCCGATTAATGAA CAATTAGGCGACACCCAGAT 832–846 1.000 73.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ATGAAATTCTTCCGCCAAGC TTAGGCGACACCCAGATTTG 842–856 1.000 72.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GCCAAGCCCCGATTAATGAA GCGACACCCAGATTTGAACT 825–839 1.000 72.5
trnC-GCA-petN_p1 trnC-GCA-petN CAAATCTGGGTGTCGCCTAA CTCCTCCCCCATACTACGAG 656–657 1.000 79.0
trnC-GCA-petN_p2 trnC-GCA-petN CAAATCTGGGTGTCGCCTAA ACGAGCGAAAGGGAAAATGT 641–642 1.000 78.9
trnC-GCA-petN_p3 trnC-GCA-petN CAAATCTGGGTGTCGCCTAA CCATACTACGAGCGAAAGGG 648–649 1.000 78.7
trnC-GCA-petN_p4 trnC-GCA-petN CAAATCTGGGTGTCGCCTAA CCCATACTACGAGCGAAAGG 649–650 1.000 78.7
trnC-GCA-petN_p5 trnC-GCA-petN CAAATCTGGGTGTCGCCTAA CCCCATACTACGAGCGAAAG 650–651 1.000 78.7
psbM-trnD-GUC_p1 psbM-trnD-GUC GCGGTAGGAACTAGAATGAACA CCTCGCTGGGATTGTAGTTC 1318–1334 1.000 64.1
psbM-trnD-GUC_p2 psbM-trnD-GUC GCGGTAGGAACTAGAATGAACA AGTTCAATCGGTCAGAGCAC 1303–1319 1.000 63.9
psbM-trnD-GUC_p3 psbM-trnD-GUC TTGACTGGCTGTTTTTACGT CCTCGCTGGGATTGTAGTTC 1355–1371 1.000 63.5
psbM-trnD-GUC_p4 psbM-trnD-GUC GCGGTAGGAACTAGAATGAACA TACACCTCGCTGGGATTGTA 1322–1338 1.000 63.4
psbM-trnD-GUC_p5 psbM-trnD-GUC TTGACTGGCTGTTTTTACGT AGTTCAATCGGTCAGAGCAC 1340–1356 1.000 63.3

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
Notholirion bulbuliferum NC_046464.1 153019 View on NCBI ↗
Notholirion campanulatum NC_058199.1 153169 View on NCBI ↗
Notholirion macrophyllum OR899322.1 152876 View on NCBI ↗
Notholirion thomsonianum NC_061550.1 152588 View on NCBI ↗