Markers + reference

Coptis

8 species · Ranunculaceae · Ranunculales

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Species 8
Genome length 154–155 kb
Candidate markers 260
Primer pairs 90

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 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbZ-trnG-GCC LSC 376 0.0466 0.99 91.2 yes View details
ndhC-trnV-UAC LSC 1171 0.0191 0.99 67.2 yes View details
petA-psbJ LSC 756 0.0141 0.98 70.2 yes View details
rpl2 IRb 1499 0.0024 1.00 41.4 no View details
ycf1-rpl32 SSC 2796 0.0119 1.00 54.1 yes View details
rpl32-trnL-UAG SSC 602 0.0179 1.00 64.0 yes View details
ndhD SSC 1530 0.0069 1.00 50.8 yes View details
rps15-trnN-GUU SSC 6444 0.0140 0.98 55.8 yes View details
rpl2 IRa 1499 0.0032 0.73 31.0 yes View details
rps19-psbA LSC 329 0.1488 0.91 82.4 no View details
ndhD-psaC SSC 97 0.0657 0.99 80.3 yes View details
rpl2-rpl23 IRb 6 0.0417 1.00 67.3 yes View details
rpl23-rpl2 IRa 6 0.0417 1.00 67.3 yes View details
trnT-UGU-trnL-UAA LSC 714 0.0119 1.00 66.5 yes View details
ndhE-ndhG SSC 249 0.0205 1.00 65.1 yes View details
ccsA-ndhD SSC 287 0.0225 0.98 65.0 yes View details
infA-rps8 LSC 121 0.0304 0.99 64.8 yes View details
petN-psbM LSC 1196 0.0090 1.00 64.4 yes View details
psbT-psbN LSC 74 0.0574 1.00 63.4 yes View details
trnL-UAG-ccsA SSC 114 0.0103 0.98 60.9 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA ACGTAAAAACGGTCAGCCAA 1054–1301 1.000 83.6
petN-psbM_p2 petN-psbM AGTAAGTCTTGCTTGGGCTG ACGTAAAAACGGTCAGCCAA 1060–1307 1.000 82.1
petN-psbM_p3 petN-psbM TCTTGCTTGGGCTGCTTTAA TACGTAAAAACGGTCAGCCA 1055–1302 1.000 82.1
petN-psbM_p4 petN-psbM AGTAAGTCTTGCTTGGGCTG TACGTAAAAACGGTCAGCCA 1061–1308 1.000 80.6
petN-psbM_p5 petN-psbM TCTTGCTTGGGCTGCTTTAA CGTAAAAACGGTCAGCCAAA 1053–1300 1.000 80.2
psbZ-trnG-GCC_p1 psbZ-trnG-GCC TGCTTCTTCTGATGGTTGGT CGTCTTCTCCTTGGCAAAGA 532–547 1.000 80.8
psbZ-trnG-GCC_p2 psbZ-trnG-GCC GCTTCTTCTGATGGTTGGTCA CGTCTTCTCCTTGGCAAAGA 531–546 1.000 78.7
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TGCTTCTTCTGATGGTTGGTC CGTCTTCTCCTTGGCAAAGA 532–547 1.000 78.7
psbZ-trnG-GCC_p4 psbZ-trnG-GCC TTGCTTCTTCTGATGGTTGGT CGTCTTCTCCTTGGCAAAGA 533–548 1.000 78.6
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TGCTTCTTCTGATGGTTGGT TACCATTCGACCATATCCGC 505–520 1.000 76.8
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 747–788 1.000 85.4
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 755–796 1.000 84.8
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 779–820 1.000 84.3
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 787–828 1.000 83.7
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG AGTCCGTAGCGTCTACCAAT 761–802 1.000 83.4
ndhC-trnV-UAC_p1 ndhC-trnV-UAC TCATATTCGTGAAGCAGAAACA AGAAGGTCTACGGTTCGAGT 1067–1242 1.000 56.3
ndhC-trnV-UAC_p2 ndhC-trnV-UAC TCATATTCGTGAAGCAGAAACA GAAGGTCTACGGTTCGAGTC 1066–1241 1.000 53.6
ndhC-trnV-UAC_p3 ndhC-trnV-UAC TCATATTCGTGAAGCAGAAACA GTTCGAGTCCGTATAGCCCT 1055–1230 1.000 52.5
ndhC-trnV-UAC_p4 ndhC-trnV-UAC CATATTCGTGAAGCAGAAACA AGAAGGTCTACGGTTCGAGT 1066–1241 1.000 52.3
ndhC-trnV-UAC_p5 ndhC-trnV-UAC TCATATTCGTGAAGCAGAAACAT AGAAGGTCTACGGTTCGAGT 1067–1242 1.000 52.3
petA-psbJ_p1 petA-psbJ GGTAATAGGGGAAGGGGTCA GCTGGTATTCTTGTGATCGGT 863–879 1.000 76.0
petA-psbJ_p2 petA-psbJ ATCCTATATACGTGGGCGGT GCTGGTATTCTTGTGATCGGT 880–896 1.000 75.7
petA-psbJ_p3 petA-psbJ GGTAATAGGGGAAGGGGTCA AGCTGGTATTCTTGTGATCGG 864–880 1.000 75.2
petA-psbJ_p4 petA-psbJ ATCCTATATACGTGGGCGGT AGCTGGTATTCTTGTGATCGG 881–897 1.000 74.9
petA-psbJ_p5 petA-psbJ CTATTTTGTCTCCGGACCCC GCTGGTATTCTTGTGATCGGT 931–947 1.000 74.5
psbT-psbN_p1 psbT-psbN TTTTCCGAGAACCACCCAAG GATCCATTCGAGGAACACGG 145 1.000 81.3
psbT-psbN_p2 psbT-psbN AGGTTCCGACTAAAAAGGCG GATCCATTCGAGGAACACGG 127 1.000 80.7
psbT-psbN_p3 psbT-psbN GGTTCCGACTAAAAAGGCGA GATCCATTCGAGGAACACGG 126 1.000 80.7
psbT-psbN_p4 psbT-psbN TTTTCCGAGAACCACCCAAG AGATCCATTCGAGGAACACG 146 1.000 80.0
psbT-psbN_p5 psbT-psbN TTTTCCGAGAACCACCCAAG GGCAACCCTCTCAACAACTA 168 1.000 79.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Coptis chinensis NC_036485.1 155484 View on NCBI ↗
Coptis chinensis var. brevisepala OM202488.1 154765 View on NCBI ↗
Coptis deltoidea NC_064406.1 154538 View on NCBI ↗
Coptis huanjiangensis OP251127.1 154640 View on NCBI ↗
Coptis japonica NC_054329.1 154985 View on NCBI ↗
Coptis omeiensis NC_054330.1 154573 View on NCBI ↗
Coptis quinquesecta NC_037759.1 154549 View on NCBI ↗
Coptis teeta NC_054331.1 154156 View on NCBI ↗