Markers + reference

Calochortus

2 species · Liliaceae · Liliales

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Species 2
Genome length 156–156 kb
Candidate markers 273
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-GCC LSC 1236 0.1861 0.87 88.7 yes View details
trnE-UUC-trnT-GGU LSC 753 0.0396 0.94 76.5 yes View details
trnT-UGU-trnL-UAA LSC 686 0.0333 0.96 73.1 yes View details
ndhC-trnV-UAC LSC 1005 0.0451 0.93 77.4 yes View details
cemA LSC 687 0.0277 1.00 62.6 yes View details
petA-psaJ LSC 838 0.0358 1.00 71.0 yes View details
psaJ-rpl33 LSC 419 0.0505 0.95 74.3 yes View details
petD-rpoA LSC 243 0.1629 0.91 76.7 yes View details
ycf1 SSC 5592 0.0235 1.00 53.4 yes View details
psbI-trnS-GCU LSC 117 0.0940 1.00 84.7 yes View details
trnM-CAU-atpE LSC 204 0.0711 0.97 80.5 yes View details
rbcL-accD LSC 884 0.0255 0.98 75.8 yes View details
atpF-atpH LSC 599 0.0383 0.87 75.0 yes View details
ndhJ-ndhK LSC 85 0.0588 1.00 74.7 yes View details
ndhE-ndhG SSC 201 0.0471 0.95 73.1 yes View details
trnF-GAA-ndhJ LSC 583 0.0312 0.93 72.2 yes View details
ndhG-ndhI SSC 363 0.0475 0.99 72.2 yes View details
rps12 IRb 798 0.0226 1.00 71.7 yes View details
rps12 IRa 798 0.0226 1.00 71.7 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU CTCCCAAGCGCACGTATTAA GATCTTACAGCGCAATCCCA 2934–2997 1.000 79.3
trnK-UUU_p2 trnK-UUU GTGCTTTCGCGTCTCTCTAA GATCTTACAGCGCAATCCCA 2998 0.500 59.5
trnK-UUU_p3 trnK-UUU GTGCTTTCGCGTCTCTCTAA TCTTACAGCGCAATCCCATT 2996 0.500 56.5
trnK-UUU_p4 trnK-UUU TTTTCAAGGACTCCCAAGCG GATCTTACAGCGCAATCCCA 2944 0.500 56.5
trnK-UUU_p5 trnK-UUU GTGCTTTCGCGTCTCTCTAA ATCTTACAGCGCAATCCCAT 2997 0.500 54.7
psbI-trnS-GCU_p1 psbI-trnS-GCU GCAATCCTGGACGTGAAGAA GGGTTCGAATCCCTCTCTCT 163–180 1.000 81.9
psbI-trnS-GCU_p2 psbI-trnS-GCU GCAATCCTGGACGTGAAGAA TTCGAATCCCTCTCTCTCCG 160–177 1.000 81.1
psbI-trnS-GCU_p3 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG GGGTTCGAATCCCTCTCTCT 427–448 1.000 80.7
psbI-trnS-GCU_p4 psbI-trnS-GCU GGGGTTGGGAGAGTTCAAAG GGGTTCGAATCCCTCTCTCT 707–728 1.000 79.8
psbI-trnS-GCU_p5 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG TTCCCGGCCATTACTTAAGC 1448 0.500 59.2
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC TAGCGGAGAGAGAGGGATTC TGAAAAACCGAAAGACCCCT 1387–1406 1.000 83.8
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC CGGAGAGAGAGGGATTCGAA TGAAAAACCGAAAGACCCCT 1384–1403 1.000 83.5
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GATAGCGGAGAGAGAGGGAT TGAAAAACCGAAAGACCCCT 1389–1408 1.000 82.0
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC TAGCGGAGAGAGAGGGATTC TGAAAAACCGAAAGACCCCTT 1387–1406 1.000 81.6
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CGGAGAGAGAGGGATTCGAA TGAAAAACCGAAAGACCCCTT 1384–1403 1.000 81.3
atpF-atpH_p1 atpF-atpH AATAGCCCAAGGAAACGCAA AATTTACGGACTGGTCGTGG 617–694 1.000 85.1
atpF-atpH_p2 atpF-atpH ATAGCCCAAGGAAACGCAAA AATTTACGGACTGGTCGTGG 616–693 1.000 85.1
atpF-atpH_p3 atpF-atpH GCCCAAGGAAACGCAAAAAT AATTTACGGACTGGTCGTGG 613–690 1.000 84.8
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG AATTTACGGACTGGTCGTGG 646–723 1.000 84.7
atpF-atpH_p5 atpF-atpH ATAGCCCAAGGAAACGCAAA TCGTGGCATTAGCGCTTTTA 602–679 1.000 83.7
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 823–840 1.000 85.5
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 821–838 1.000 85.5
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 877–894 1.000 85.2
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 802–819 1.000 85.1
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 800–817 1.000 85.1
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CCGTAGCGTCTACCGATTTC 733–747 1.000 82.0
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA AAAGCCAGCTATCGGAATCG CCGTAGCGTCTACCGATTTC 778–792 1.000 81.8
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT CCGTAGCGTCTACCGATTTC 765–779 1.000 81.0
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CGTCTACCGATTTCGCCATA 727–741 1.000 80.8
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA AAAGCCAGCTATCGGAATCG CGTCTACCGATTTCGCCATA 772–786 1.000 80.5

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
Calochortus uniflorus NC_058300.1 155794 View on NCBI ↗
Calochortus venustus MT261150.1 155688 View on NCBI ↗