Markers + reference

Tinospora

2 species · Menispermaceae · Ranunculales

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Species 2
Genome length 151–161 kb
Candidate markers 245
Primer pairs 60

Genome-wide nucleotide diversity

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

Candidate markers

3 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 245 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoC2 LSC 4242 0.4562 0.81 75.5 yes View details
psbB LSC 1527 0.4453 0.44 71.8 yes View details
psbB LSC 1527 0.0020 1.00 48.6 no View details
psbC-trnS-TGA LSC 195 0.0568 0.90 83.6 yes View details
trnH-GTG-psbA LSC 172 0.0640 1.00 83.0 yes View details
rps15-ycf1 SSC 451 0.0312 1.00 74.0 yes View details
ndhF-rpl32 SSC 703 0.0343 0.99 73.4 yes View details
psbM LSC 117 0.4530 1.00 72.6 yes View details
trnF-GAA-ndhJ LSC 736 0.0246 0.99 71.7 yes View details
trnP-TGG-psaJ LSC 313 0.0415 1.00 70.4 yes View details
petD-rpoA LSC 188 0.0270 0.98 69.5 yes View details
psbI-trnS-GCT LSC 140 0.0357 1.00 69.0 yes View details
atpB-rbcL LSC 809 0.0115 0.97 68.6 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 60 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GTG-psbA_p1 trnH-GTG-psbA CTGCCTTAATCCACTTGGCT CAACCGTGCTAACCTTGGTA 300–658 1.000 79.4
trnH-GTG-psbA_p2 trnH-GTG-psbA CTGCCTTAATCCACTTGGCT AAGCCCCATCTACAAATGGC 223–581 1.000 79.4
trnH-GTG-psbA_p3 trnH-GTG-psbA CTGCCTTAATCCACTTGGCT ATCAACCGTGCTAACCTTGG 302–660 1.000 79.3
trnH-GTG-psbA_p4 trnH-GTG-psbA ACTGCCTTAATCCACTTGGC CAACCGTGCTAACCTTGGTA 301–659 1.000 79.2
trnH-GTG-psbA_p5 trnH-GTG-psbA ACTGCCTTAATCCACTTGGC ATCAACCGTGCTAACCTTGG 303–661 1.000 79.1
psbI-trnS-GCT_p1 psbI-trnS-GCT CCCCCATGCTTACTCTCAAA TAAAGCGGCGGATTGCTAAT 324 0.500 53.2
psbI-trnS-GCT_p2 psbI-trnS-GCT CCCCCATGCTTACTCTCAAA ATTGGGAGAGATGGCTGAGT 348 0.500 52.7
psbI-trnS-GCT_p3 psbI-trnS-GCT CCCCCATGCTTACTCTCAAA ATGGCTGAGTGGACTAAAGC 338 0.500 50.3
psbI-trnS-GCT_p4 psbI-trnS-GCT CCCCCATGCTTACTCTCAAA GAGAGATGGCTGAGTGGACT 343 0.500 49.4
psbI-trnS-GCT_p5 psbI-trnS-GCT CCCCATGCTTACTCTCAAACT TAAAGCGGCGGATTGCTAAT 323 0.500 48.8
rpoC2_p1 rpoC2 ACGGTCGAAGCCATTACTTC CCCATTTCGAGGACTCACAG 803 0.500 59.8
rpoC2_p2 rpoC2 ACGGTCGAAGCCATTACTTC ATTGGTTGTGCTCGAAAGGT 952 0.500 59.8
rpoC2_p3 rpoC2 ACGGTCGAAGCCATTACTTC CCCGGTTCCCCAATAGATTG 1093 0.500 59.8
rpoC2_p4 rpoC2 GGGTCGATCTGGTCTTTCAC CCCATTTCGAGGACTCACAG 689 0.500 59.8
rpoC2_p5 rpoC2 GGGTCGATCTGGTCTTTCAC ATTGGTTGTGCTCGAAAGGT 838 0.500 59.8
psbM_p1 psbM CGAGAGCAACTAGAGTCGTC CGTGCTGCTCTCACTAAAGT 1245–2469 1.000 79.7
psbM_p2 psbM TGATGATTCTAGCCCGCTCA CGTGCTGCTCTCACTAAAGT 867–1642 1.000 79.1
psbM_p3 psbM CCCTCTCTACTGTTCAGGGA CGTGCTGCTCTCACTAAAGT 1309–2533 1.000 78.9
psbM_p4 psbM TCCCTCTCTACTGTTCAGGG CGTGCTGCTCTCACTAAAGT 1310–2534 1.000 78.9
psbM_p5 psbM CGAGAGCAACTAGAGTCGTC ATAGACAATAGCCGTGCTGC 1257 0.500 55.4
psbC-trnS-TGA_p1 psbC-trnS-TGA AGCTGCAGCAGGATTTGAAA GGTTGATAGCTCCGGTCTTG 330–345 1.000 82.9
psbC-trnS-TGA_p2 psbC-trnS-TGA GCTGCAGCAGGATTTGAAAA GGTTGATAGCTCCGGTCTTG 329–344 1.000 82.4
psbC-trnS-TGA_p3 psbC-trnS-TGA AGCTGCAGCAGGATTTGAAA GATGGCCGAGTGGTTGATAG 341–356 1.000 82.3
psbC-trnS-TGA_p4 psbC-trnS-TGA AGCTGCAGCAGGATTTGAAA GGGTTCGAATCCCTCTCTCT 276–291 1.000 82.1
psbC-trnS-TGA_p5 psbC-trnS-TGA GCTGCAGCAGGATTTGAAAA GATGGCCGAGTGGTTGATAG 340–355 1.000 81.7
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA GAAAGCTGGATAGGATGGCC 845–883 1.000 80.8
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ GCCCAAGCCCTCTAGTAGTA GAAAGCTGGATAGGATGGCC 926–964 1.000 80.4
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA ATCATCCACGCTTGAAACGT 877–915 1.000 80.0
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ GCCCAAGCCCTCTAGTAGTA ATCATCCACGCTTGAAACGT 958–996 1.000 79.6
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA TTTGATGCCTGAAAGCTGGA 855–893 1.000 79.3

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
Tinospora cordifolia NC_042153.1 150945 View on NCBI ↗
Tinospora sinensis PV747743.1 160664 View on NCBI ↗