Markers + reference

Sarcandra

2 species · Chloranthaceae · Chloranthales

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Species 2
Genome length 159–159 kb
Candidate markers 267
Primer pairs 80

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 6 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5658 0.3343 0.85 74.7 yes View details
rps15 SSC 264 0.5085 0.89 75.8 yes View details
ndhH SSC 1188 0.4947 0.80 79.6 yes View details
ndhA SSC 2181 0.4769 0.85 79.5 yes View details
ndhE SSC 303 0.4875 0.93 76.8 yes View details
psaC SSC 246 0.4689 0.85 74.6 yes View details
ndhD SSC 1503 0.4816 0.85 80.8 yes View details
ccsA SSC 963 0.4800 0.88 81.8 yes View details
trnL-UAG-rpl32 SSC 936 0.4588 0.83 80.6 yes View details
ndhF SSC 2223 0.4757 0.88 80.1 yes View details
psbT-psbN LSC 66 0.1212 1.00 87.5 yes View details
rpl32-ndhF SSC 1113 0.4378 0.90 82.3 yes View details
ndhI SSC 558 0.4563 0.90 81.4 yes View details
ndhG SSC 531 0.4296 0.78 77.3 yes View details
ndhG-ndhE SSC 259 0.4735 0.95 77.3 yes View details
psaC-ndhD SSC 127 0.4590 0.96 76.3 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbT-psbN_p1 psbT-psbN TTTTCGAGAACCACCCAAGG TCGCCATCTCCATATCTGGT 222 1.000 82.6
psbT-psbN_p2 psbT-psbN TTTTCGAGAACCACCCAAGG CCCTAGTCGCCATCTCCATA 228 1.000 82.0
psbT-psbN_p3 psbT-psbN TTTTCGAGAACCACCCAAGG GATCCATTCGAGGAACACGG 136 1.000 81.1
psbT-psbN_p4 psbT-psbN TTTTCGAGAACCACCCAAGG GGGTACGCCTTATATACCGC 184 1.000 81.0
psbT-psbN_p5 psbT-psbN TTTTCGAGAACCACCCAAGG GTCGCCATCTCCATATCTGG 223 1.000 79.7
ycf1_p1 ycf1 AAGAGGGATCCACCGAAGAA CGGTTCATTCCCCATCCAAT 1508 0.500 59.0
ycf1_p2 ycf1 TTGCACACATGTCCAAGTGA CGGTTCATTCCCCATCCAAT 1170 0.500 59.0
ycf1_p3 ycf1 AAGAGGGATCCACCGAAGAA CACCTCTTCTGCTCGATCAC 1289 0.500 59.0
ycf1_p4 ycf1 AAGAGGGATCCACCGAAGAA CCGTTCATCCTCGTCTTGTT 1592 0.500 59.0
ycf1_p5 ycf1 TTGCACACATGTCCAAGTGA CACCTCTTCTGCTCGATCAC 951 0.500 59.0
rps15_p1 rps15 CCAGATCGAAATGACTGGCA GAAAGGAGTCTGTGCACCAA 850 0.500 59.5
rps15_p2 rps15 CCAGATCGAAATGACTGGCA TTCCTCTCCGCCAATAATGC 1096 0.500 59.5
rps15_p3 rps15 ACCAGATCGAAATGACTGGC GAAAGGAGTCTGTGCACCAA 851 0.500 59.5
rps15_p4 rps15 ACCAGATCGAAATGACTGGC TTCCTCTCCGCCAATAATGC 1097 0.500 59.5
rps15_p5 rps15 CCAGATCGAAATGACTGGCA AACACCATGCATTGATGGGT 532 0.500 59.3
ndhH_p1 ndhH GAAAACGTCAACGACTGCTG TACGTTGTTGTATCCCTGCG 1578 0.500 60.0
ndhH_p2 ndhH CCAGATCGAAATGACTGGCA TACGTTGTTGTATCCCTGCG 1824 0.500 59.8
ndhH_p3 ndhH ACCAGATCGAAATGACTGGC TACGTTGTTGTATCCCTGCG 1825 0.500 59.8
ndhH_p4 ndhH GAAAACGTCAACGACTGCTG TGTTCCAACGAATCACACGT 1965 0.500 59.5
ndhH_p5 ndhH CCAGATCGAAATGACTGGCA TGTTCCAACGAATCACACGT 2211 0.500 59.3
ndhA_p1 ndhA ATGGAGATGGAAAATCCGCC TTGGACAATACTCGACGCAG 2747 0.500 59.8
ndhA_p2 ndhA CAGGCTCTGGAAGGAATTCC TTGGACAATACTCGACGCAG 2965 0.500 59.5
ndhA_p3 ndhA ATGGAGATGGAAAATCCGCC TGCAGCTCGTACTGTTTGTT 2458 0.500 59.5
ndhA_p4 ndhA ATGGAGATGGAAAATCCGCC TTGCAGCTCGTACTGTTTGT 2459 0.500 59.5
ndhA_p5 ndhA ATGGAGATGGAAAATCCGCC AACCCAGTCACCATAGGGAA 2424 0.500 59.5
ndhI_p1 ndhI CATCGAGGAGCCGTATGAAG GACATTTATGGCTCCCACGT 1807 0.500 59.2
ndhI_p2 ndhI GCGGGTGGAATTTCCCTATT GACATTTATGGCTCCCACGT 1448 0.500 59.2
ndhI_p3 ndhI CATCGAGGAGCCGTATGAAG CATGACCTTACTTACCGGGC 1554 0.500 59.1
ndhI_p4 ndhI ACCCTACAAACATGCCAAGG GACATTTATGGCTCCCACGT 1861 0.500 59.1
ndhI_p5 ndhI CCCTACAAACATGCCAAGGT GACATTTATGGCTCCCACGT 1860 0.500 59.1

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
Sarcandra glabra NC_039621.1 158900 View on NCBI ↗
Sarcandra glabra subsp. brachystachys OR909482.1 158826 View on NCBI ↗