Markers + reference

Chionographis

3 species · Melanthiaceae · Liliales

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Species 3
Genome length 155–157 kb
Candidate markers 274
Primer pairs 105

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 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 666 0.0152 0.92 69.3 yes View details
rps16-trnQ-UUG LSC 574 0.0108 0.59 59.1 yes View details
psbK-psbI LSC 413 0.0265 0.98 73.1 yes View details
rpoB-trnC-GCA LSC 964 0.0110 0.98 61.4 yes View details
petA-psbJ LSC 1101 0.0143 0.99 59.7 yes View details
petL-petG LSC 199 0.0121 0.97 59.5 yes View details
rpl20-rps12 LSC 777 0.0060 1.00 50.3 yes View details
ndhF SSC 2223 0.0093 1.00 48.2 yes View details
ndhF-rpl32 SSC 742 0.0144 1.00 54.0 yes View details
rpl32-trnL-UAG SSC 863 0.0145 0.98 61.2 yes View details
rps15-ycf1 SSC 428 0.0255 0.98 68.4 yes View details
petG-trnW-CCA LSC 121 0.0606 1.00 79.5 yes View details
psbT-psbN LSC 60 0.0778 1.00 68.6 yes View details
psbE-petL LSC 1203 0.0084 0.99 65.2 yes View details
trnF-GAA-ndhJ LSC 748 0.0054 1.00 63.3 yes View details
ndhC-trnV-UAC LSC 828 0.0064 1.00 62.9 yes View details
rpl14-rpl16 LSC 129 0.0271 0.95 62.7 yes View details
petN-psbM LSC 1011 0.0033 0.99 62.4 yes View details
rpl36-infA LSC 106 0.0314 1.00 62.3 yes View details
rps12-trnV-GAC IRb 1810 0.0037 0.99 61.5 yes View details
trnV-GAC-rps12 IRa 1810 0.0037 0.99 61.5 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 105 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 797 0.333 50.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 CATAGCCGCACTTAAAAGCC TTTTCTTGAAAACGGCGCTC 802 0.333 48.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GCGCTCAACCTACAGTAACT 783 0.333 48.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 TGTGAAAGATCATAGCCGCA TTTTCTTGAAAACGGCGCTC 812 0.333 46.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 CATAGCCGCACTTAAAAGCC GCGCTCAACCTACAGTAACT 788 0.333 46.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 665 0.333 52.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 663 0.333 52.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 671 0.333 52.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GAATCCACAGCCGATCATGT GAGGTTCGAATCCTTCCGTC 672 0.333 52.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 647 0.333 51.6
psbK-psbI_p1 psbK-psbI GCTGCTGCAAGTTTTCGATG GGATTGCGTCCTGGATCATT 525–529 1.000 78.6
psbK-psbI_p2 psbK-psbI AGCTGCTGCAAGTTTTCGAT GGATTGCGTCCTGGATCATT 526–530 1.000 77.8
psbK-psbI_p3 psbK-psbI CTTTGTTTGGCAAGCTGCTG GGATTGCGTCCTGGATCATT 538–542 1.000 77.5
psbK-psbI_p4 psbK-psbI GCTGCTGCAAGTTTTCGATG TATTCCTCACGTCCGGGATT 540–544 1.000 76.9
psbK-psbI_p5 psbK-psbI GCTGCTGCAAGTTTTCGATG TTATTCCTCACGTCCGGGAT 541–545 1.000 76.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG AAAGGATTTGCAGTCCCCTG 902–1111 1.000 83.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TAAATCCGGGTATTGTGGGC AAAGGATTTGCAGTCCCCTG 844–1053 1.000 81.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG GCCAATTTGTTCATCAGGCG 945–1154 1.000 80.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AAATTCTTCCGTCAAGCCCT AAAGGATTTGCAGTCCCCTG 903–1112 1.000 79.8
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CAAATTCTTCCGTCAAGCCC AAAGGATTTGCAGTCCCCTG 904–1113 1.000 79.4
petN-psbM_p1 petN-psbM CCCTTTCACTCGTGGTATGG ACGTAAAAACAGTCAGCCAA 1078–1093 1.000 64.4
petN-psbM_p2 petN-psbM CCTTTCACTCGTGGTATGGG ACGTAAAAACAGTCAGCCAA 1077–1092 1.000 64.4
petN-psbM_p3 petN-psbM CTTTCACTCGTGGTATGGGG ACGTAAAAACAGTCAGCCAA 1076–1091 1.000 64.4
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT ACGTAAAAACAGTCAGCCAA 1123–1138 1.000 63.3
petN-psbM_p5 petN-psbM CTTTCACTCGTGGTATGGGG TCTACGTAAAAACAGTCAGCCA 1079–1094 1.000 63.3
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ GGTTGGGATAGCTCAGTTGG TCTTGATGCCCGAAAGTTGG 900–908 1.000 77.2
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA TCTTGATGCCCGAAAGTTGG 860–868 1.000 77.1
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ GGTTGGGATAGCTCAGTTGG AAACGTATCTTGATGCCCGA 907–915 1.000 75.4
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ GGTTGGGATAGCTCAGTTGG AACGTATCTTGATGCCCGAA 906–914 1.000 75.4
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ GGTTGGGATAGCTCAGTTGG ACGTATCTTGATGCCCGAAA 905–913 1.000 75.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Chionographis chinensis PV786079.1 156924 View on NCBI ↗
Chionographis japonica PV786082.1 154657 View on NCBI ↗
Chionographis koidzumiana PV786083.1 155324 View on NCBI ↗