Markers + reference

Veratrum

10 species · Melanthiaceae · Liliales

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Species 10
Genome length 152–154 kb
Candidate markers 268
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-trnQ-UUG LSC 2361 0.0156 0.47 43.4 yes View details
psbK-psbI LSC 477 0.0291 0.84 55.2 yes View details
trnS-GCU-trnG-UCC LSC 914 0.0263 0.93 62.1 yes View details
rpoB-trnC-GCA LSC 935 0.0214 0.98 53.0 yes View details
trnT-GGU-psbD LSC 823 0.0213 0.98 54.7 yes View details
trnT-UGU-trnL-UAA LSC 761 0.0283 0.97 74.0 yes View details
trnP-UGG-psaJ LSC 413 0.0332 0.94 59.3 yes View details
rpl16 LSC 1376 0.0165 1.00 51.7 yes View details
ycf1 SSC 5397 0.0170 1.00 52.9 yes View details
ycf1-rps15 SSC 384 0.0346 1.00 54.7 yes View details
trnL-UAG-rpl32 SSC 637 0.0237 0.96 62.2 yes View details
ndhF SSC 2199 0.0173 1.00 48.0 yes View details
ycf1 IRa 1017 0.0052 1.00 40.3 no View details
psbT-psbN LSC 64 0.0316 1.00 66.8 yes View details
psbI-trnS-GCU LSC 124 0.0595 0.96 64.9 yes View details
ycf4-cemA LSC 712 0.0231 0.98 60.3 yes View details
atpH-atpI LSC 756 0.0182 1.00 59.2 yes View details
ndhA-ndhI SSC 82 0.0336 1.00 59.0 yes View details
petD-rpoA LSC 130 0.0574 1.00 58.2 yes View details
rpl32-ndhF SSC 523 0.0260 0.85 57.6 yes View details
rpl22-rps19 LSC 84 0.0317 1.00 56.5 yes View details
ndhC-trnV-UAC LSC 1224 0.0199 0.99 55.8 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG CCTTTCAGGATCAGTCGTGG TTTGGGCTGGAATTGACGAA 1374–2631 1.000 87.5
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG TCAGGATCAGTCGTGGTCTT TTTGGGCTGGAATTGACGAA 1370–2627 1.000 87.1
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG TTCAGGATCAGTCGTGGTCT TTTGGGCTGGAATTGACGAA 1371–2628 1.000 87.1
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG CTGTCCCCTTCCAAAAACCA TTTGGGCTGGAATTGACGAA 1526–2784 1.000 86.9
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG CCTTTCAGGATCAGTCGTGG GAGGTTCGAATCCTTCCGTC 1268–2516 0.800 78.5
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGAATAGTTTGAGAGTAAGCA 444–531 1.000 51.2
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGAATAGTTTGAGAGTAAGCA 441–528 1.000 49.8
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT ACGAATAGTTTGAGAGTAAGCA 442–529 1.000 49.8
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT ACGAATAGTTTGAGAGTAAGCA 443–530 1.000 49.8
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG AACGAATAGTTTGAGAGTAAGCA 445–532 1.000 49.7
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TAAAGCGGCGGATTGCTAAT 200–221 1.000 81.9
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA ATTCGGAGAGATGGCTGAGT 224–245 1.000 79.9
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA TAAAGCGGCGGATTGCTAAT 200–221 1.000 79.5
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA ATGGCTGAGTGGACTAAAGC 214–235 1.000 78.5
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA ATTCGGAGAGATGGCTGAGT 224–245 1.000 77.6
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 925–988 1.000 60.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 926–989 1.000 58.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT ACGAATCACACTTTTACCACT 911–974 1.000 57.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA TACCACTAAACTATACCCGC 911–974 1.000 56.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC ACGAATCACACTTTTACCACT 906–969 1.000 56.3
atpH-atpI_p1 atpH-atpI ACGGAAGCGGCAGAAATTAT CGAATCCATGGAGGGTCATC 810–821 0.800 73.6
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 813–824 0.800 73.6
atpH-atpI_p3 atpH-atpI TACCTTCTACAGCTTGGCCT CGAATCCATGGAGGGTCATC 896–907 0.800 73.2
atpH-atpI_p4 atpH-atpI AACGGAAGCGGCAGAAATTA CGAATCCATGGAGGGTCATC 811–822 0.800 72.5
atpH-atpI_p5 atpH-atpI TAACGGAAGCGGCAGAAATT CGAATCCATGGAGGGTCATC 812–823 0.800 72.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCCGCCTACACAAGCAAATT AACTTGTTTAGCAGGCGACA 1723–1727 1.000 82.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCCGCCTACACAAGCAAATT GATTTCTCGTCGGCCTATCC 2181–2185 1.000 82.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCCGCCTACACAAGCAAATT GGATTTCTCGTCGGCCTATC 2182–2186 1.000 82.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCCGCCTACACAAGCAAATT TTCAGCCCTTTCCACTCCTA 2207–2211 0.800 74.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCCGCCTACACAAGCAAATT AATGGCTCGAACCAATCCTC 1946 0.100 42.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Veratrum dahuricum NC_061625.1 153688 View on NCBI ↗
Veratrum grandiflorum NC_061622.1 153711 View on NCBI ↗
Veratrum japonicum NC_041306.1 151791 View on NCBI ↗
Veratrum maackii NC_061620.1 151597 View on NCBI ↗
Veratrum mengtzeanum NC_045300.1 152051 View on NCBI ↗
Veratrum nanchuanense NC_061621.1 153692 View on NCBI ↗
Veratrum nigrum NC_061624.1 151599 View on NCBI ↗
Veratrum oblongum NC_061623.1 151767 View on NCBI ↗
Veratrum schindleri NC_061618.1 151768 View on NCBI ↗
Veratrum stenophyllum NC_061619.1 152028 View on NCBI ↗