Markers + reference

Chloranthus

7 species · Chloranthaceae · Chloranthales

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Species 7
Genome length 158–159 kb
Candidate markers 267
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 901 0.0453 0.97 83.9 yes View details
atpF-atpH LSC 471 0.0575 1.00 82.0 yes View details
atpI-rps2 LSC 358 0.0537 0.67 67.6 yes View details
trnT-UGU-trnL-UAA LSC 741 0.0457 0.99 79.1 yes View details
accD-psaI LSC 674 0.0380 0.96 70.2 yes View details
clpP LSC 2078 0.0137 0.99 56.1 yes View details
ycf1 SSC 5637 0.0156 1.00 51.9 yes View details
trnL-UAG-rpl32 SSC 947 0.0355 1.00 73.8 yes View details
rpl32-ndhF SSC 1164 0.0307 0.99 75.6 yes View details
ndhF SSC 2220 0.0159 1.00 49.0 yes View details
psbZ-trnG-GCC LSC 354 0.0344 1.00 71.1 yes View details
trnD-GUC-trnY-GUA LSC 346 0.0447 0.93 69.4 yes View details
rpoB-trnC-GCA LSC 1173 0.0188 0.98 68.0 yes View details
rpl16-rps3 LSC 155 0.0357 1.00 66.3 yes View details
ccsA-trnL-UAG SSC 101 0.0514 1.00 65.9 yes View details
ndhC-trnV-UAC LSC 1723 0.0184 0.99 65.5 yes View details
ndhD-ccsA SSC 257 0.0341 0.97 63.9 yes View details
ycf4-cemA LSC 938 0.0213 0.98 63.3 yes View details
rpl33-rps18 LSC 155 0.0337 1.00 62.7 yes View details
rpl20-rps12 LSC 767 0.0162 0.99 61.9 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC AATCTGCCGCTTTAGTCCAC ACGAATCACACTTTTACCACT 941–1080 1.000 60.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCTGCCGCTTTAGTCCA ACGAATCACACTTTTACCACT 942–1081 1.000 60.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATCAGAAGGAGCGGAGAGAG ACGAATCACACTTTTACCACT 1006–1145 1.000 60.0
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GATCAGAAGGAGCGGAGAGA ACGAATCACACTTTTACCACT 1007–1146 1.000 60.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA ACGAATCACACTTTTACCACT 995–1134 1.000 60.0
atpF-atpH_p1 atpF-atpH CCAGTAACCCACGGAAACAA AGCAGAGGGTAAAATACGCG 573–650 1.000 91.2
atpF-atpH_p2 atpF-atpH CCAGTAACCCACGGAAACAA AATTTACGGACTGGTCGTGG 513–590 1.000 91.0
atpF-atpH_p3 atpF-atpH CCAGTAACCCACGGAAACAA TCGTGGCATTAGCGCTTTTA 499–576 1.000 89.6
atpF-atpH_p4 atpF-atpH CCAGTAACCCACGGAAACAA CAGAGGGTAAAATACGCGGT 571–648 1.000 89.3
atpF-atpH_p5 atpF-atpH GACCAGTAACCCACGGAAAC AGCAGAGGGTAAAATACGCG 575–652 1.000 87.6
atpI-rps2_p1 atpI-rps2 GCGATTACGACCCAAGAAGT CTTTGGGGATTCCGACGATT 530–668 1.000 88.2
atpI-rps2_p2 atpI-rps2 GCGATTACGACCCAAGAAGT ATCAGCTGCAATAAGGGCTC 820–958 1.000 87.0
atpI-rps2_p3 atpI-rps2 GCGATTACGACCCAAGAAGT GGGCTCGGTGTCATTATGTT 806–944 1.000 86.9
atpI-rps2_p4 atpI-rps2 GGAAACCCCCTATTTGCCAA ATCAGCTGCAATAAGGGCTC 777–915 1.000 86.7
atpI-rps2_p5 atpI-rps2 TTGGAAACCCCCTATTTGCC ATCAGCTGCAATAAGGGCTC 779–917 1.000 86.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCG CTGGGGAGAAAGGATTTGCA 1208–1262 1.000 79.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCG TGGGGAGAAAGGATTTGCAG 1207–1261 1.000 79.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCG ACTGGGGAGAAAGGATTTGC 1209–1263 1.000 79.6
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCG AGAAAGGATTTGCAGTCCCC 1202–1256 1.000 79.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCG GGGGAGAAAGGATTTGCAGT 1206–1260 1.000 79.6
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA TTCATCGGATCCTAGGTCGG GGGGACGGACTGTAAATTCG 449–498 1.000 83.0
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 388–437 1.000 83.0
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA TTCATCGGATCCTAGGTCGG GGGACGGACTGTAAATTCGT 448–497 1.000 82.8
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 387–436 1.000 82.8
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA TTCATCGGATCCTAGGTCGG GATTCTTCCTGGGTCGATGC 482–531 1.000 82.2
psbZ-trnG-GCC_p1 psbZ-trnG-GCC GGTACGTCGTTATGGATTGGA TACATCACCATGGGCGGATA 458–514 1.000 74.6
psbZ-trnG-GCC_p2 psbZ-trnG-GCC GGTACGTCGTTATGGATTGGA GATCGAACCCGCATCTTCTC 433–489 1.000 73.0
psbZ-trnG-GCC_p3 psbZ-trnG-GCC GGTACGTCGTTATGGATTGGA GAACCCGCATCTTCTCCTTG 429–485 1.000 72.1
psbZ-trnG-GCC_p4 psbZ-trnG-GCC GGTACGTCGTTATGGATTGGA TACCATTCGACCATATCCGC 395–451 1.000 71.6
psbZ-trnG-GCC_p5 psbZ-trnG-GCC GGTACGTCGTTATGGATTGGA TATACATCACCATGGGCGGA 502 0.286 37.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Chloranthus erectus NC_039627.1 157852 View on NCBI ↗
Chloranthus henryi PQ728881.1 157957 View on NCBI ↗
Chloranthus nervosus NC_082096.1 158002 View on NCBI ↗
Chloranthus oldhamii PQ728884.1 157705 View on NCBI ↗
Chloranthus serratus NC_026565.1 158640 View on NCBI ↗
Chloranthus sessilifolius PQ728886.1 157614 View on NCBI ↗
Chloranthus spicatus NC_009598.1 157772 View on NCBI ↗