Markers + reference

Chamaelirium

2 species · Melanthiaceae · Liliales

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Species 2
Genome length 157–158 kb
Candidate markers 274
Primer pairs 90

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 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 418 0.0219 0.98 62.9 yes View details
atpF-atpH LSC 501 0.0343 0.99 65.5 yes View details
trnT-UGU-trnL-UAA LSC 819 0.0245 1.00 63.3 yes View details
petA-psbJ LSC 1106 0.0272 1.00 67.4 yes View details
infA LSC 234 0.0128 1.00 45.1 yes View details
ndhF SSC 2229 0.0194 0.99 55.9 yes View details
ndhF-rpl32 SSC 760 0.0286 0.96 69.4 yes View details
rpl32-trnL-UAG SSC 868 0.0278 0.95 73.0 yes View details
rps15-ycf1 SSC 427 0.0445 1.00 78.2 yes View details
psbT-psbN LSC 60 0.1167 1.00 74.8 yes View details
ndhC-trnV-UAC LSC 1041 0.0189 0.97 72.8 yes View details
rpl36-infA LSC 106 0.0660 1.00 71.8 yes View details
atpH-atpI LSC 624 0.0194 0.99 69.5 yes View details
infA-rps8 LSC 124 0.0403 1.00 68.6 yes View details
trnK-UUU-rps16 LSC 719 0.0261 0.91 67.3 yes View details
psbE-petL LSC 1201 0.0183 1.00 66.9 yes View details
psaA-ycf3 LSC 647 0.0094 0.98 64.5 yes View details
rpl22-psbA IRa 252 0.0442 0.99 64.4 no View details
psbI-trnS-GCU LSC 151 0.0331 1.00 63.9 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 CCGCACTTAAAAGCCGAGTA TTTTCTTGAAAACGGCGCTC 782–850 1.000 82.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 CATAGCCGCACTTAAAAGCC TTTTCTTGAAAACGGCGCTC 787–855 1.000 80.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GCGCTCAACCTACAGTAACT 768–836 1.000 80.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 TGTGAAAGATCATAGCCGCA TTTTCTTGAAAACGGCGCTC 797–865 1.000 79.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 CATAGCCGCACTTAAAAGCC GCGCTCAACCTACAGTAACT 773–841 1.000 79.0
psbK-psbI_p1 psbK-psbI GCTGCTGCAAGTTTTCGATG GGATTGCGTCCTGGATCATT 528–534 1.000 76.9
psbK-psbI_p2 psbK-psbI AGCTGCTGCAAGTTTTCGAT GGATTGCGTCCTGGATCATT 529–535 1.000 76.1
psbK-psbI_p3 psbK-psbI CTTTGTTTGGCAAGCTGCTG GGATTGCGTCCTGGATCATT 541–547 1.000 75.9
psbK-psbI_p4 psbK-psbI GCTGCTGCAAGTTTTCGATG TATTCCTCACGTCCGGGATT 543–549 1.000 75.3
psbK-psbI_p5 psbK-psbI GCTGCTGCAAGTTTTCGATG TTATTCCTCACGTCCGGGAT 544–550 1.000 75.3
psbI-trnS-GCU_p1 psbI-trnS-GCU AATCCCGGACGTGAGGAATA TAAAGCGGCGGATTGCTAAT 240 1.000 79.6
psbI-trnS-GCU_p2 psbI-trnS-GCU ATCCCGGACGTGAGGAATAA TAAAGCGGCGGATTGCTAAT 239 1.000 79.6
psbI-trnS-GCU_p3 psbI-trnS-GCU AATCCCGGACGTGAGGAATA GGGTTCGAATCCCTCTCTCT 195 1.000 78.6
psbI-trnS-GCU_p4 psbI-trnS-GCU ATCCCGGACGTGAGGAATAA GGGTTCGAATCCCTCTCTCT 194 1.000 78.6
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCCCGGACGTGAGGAATAA TTCGAATCCCTCTCTCTCCG 191 1.000 77.8
atpF-atpH_p1 atpF-atpH ATAGCCCAAGGAAACAAAAA ATTTATGGACTGGTCGTGGC 593–594 1.000 44.4
atpF-atpH_p2 atpF-atpH ATAGCCCAAGGAAACAAAAA TCGTGGCATTAGCGCTTTTA 580–581 1.000 43.2
atpF-atpH_p3 atpF-atpH ATAGCCCAAGGAAACAAAAA CGTGGCATTAGCGCTTTTAT 579–580 1.000 43.2
atpF-atpH_p4 atpF-atpH ATAGCCCAAGGAAACAAAAA CGTGGCATTAGCGCTTTTATT 579–580 1.000 43.2
atpF-atpH_p5 atpF-atpH ATAGCCCAAGGAAACAAAAA GGACTGGTCGTGGCATTAG 587–588 1.000 43.1
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 681–948 1.000 80.0
atpH-atpI_p2 atpH-atpI AATAACGGAAGCGGCAGAAA CGAATCCATGGAGGGTCATC 682–949 1.000 78.8
atpH-atpI_p3 atpH-atpI GCCAATCCAGCAGCAATAAC CGAATCCATGGAGGGTCATC 696–963 1.000 78.5
atpH-atpI_p4 atpH-atpI TCCAGCAGCAATAACGGAAG CGAATCCATGGAGGGTCATC 691–958 1.000 78.1
atpH-atpI_p5 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 712–979 1.000 77.2
psaA-ycf3_p1 psaA-ycf3 AGACGTTTTTACGGGATCCC ATTGGTTGAAGATCACGGGG 739–751 1.000 77.8
psaA-ycf3_p2 psaA-ycf3 GACGTTTTTACGGGATCCCT ATTGGTTGAAGATCACGGGG 738–750 1.000 77.8
psaA-ycf3_p3 psaA-ycf3 CTGGCCCATTCGTCAAAAGA ATTGGTTGAAGATCACGGGG 756–768 1.000 77.1
psaA-ycf3_p4 psaA-ycf3 TCTGGCCCATTCGTCAAAAG ATTGGTTGAAGATCACGGGG 757–769 1.000 77.1
psaA-ycf3_p5 psaA-ycf3 TGTTCTTGAGAAATGGCCCG ATTGGTTGAAGATCACGGGG 778–790 1.000 77.1

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
Chamaelirium luteum PV786081.1 157655 View on NCBI ↗
Chamaelirium viridiflorum PV786080.1 157087 View on NCBI ↗