Markers + reference

Parnassia

26 species · Celastraceae · Celastrales

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Species 26
Genome length 151–154 kb
Candidate markers 279
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 279 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 781 0.0385 0.96 74.3 yes View details
trnS-GCU-trnG-UCC LSC 916 0.0519 0.98 85.3 yes View details
trnG-UCC-trnR-UCU LSC 410 0.0524 0.98 85.3 yes View details
trnT-GGU-psbD LSC 1294 0.0275 0.98 73.9 yes View details
psbZ-trnG-GCC LSC 826 0.0296 0.98 74.3 yes View details
atpB-rbcL LSC 872 0.0290 0.98 80.8 yes View details
petA-psbJ LSC 573 0.0375 1.00 74.3 yes View details
ndhF SSC 2244 0.0167 1.00 59.3 yes View details
ndhF-rpl32 SSC 952 0.0375 0.98 78.0 yes View details
rps15-ycf1 SSC 317 0.0428 0.95 71.6 yes View details
psbM-trnD-GUC LSC 854 0.0265 0.98 80.3 yes View details
rps11-rpl36 LSC 278 0.0450 0.96 77.0 yes View details
rps4-trnT-UGU LSC 674 0.0279 1.00 75.9 yes View details
trnH-GUG-psbA LSC 302 0.0540 0.97 75.5 yes View details
trnT-UGU-trnL-UAA LSC 579 0.0287 0.99 75.5 yes View details
atpH-atpI LSC 632 0.0310 1.00 74.8 yes View details
psbK-psbI LSC 369 0.0386 0.96 74.6 yes View details
psbE-petL LSC 1295 0.0245 0.99 74.5 yes View details
trnL-UAG-ccsA SSC 139 0.0740 0.99 74.2 yes View details
ccsA-ndhD SSC 227 0.0519 0.94 74.2 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 369–558 1.000 90.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 383–572 1.000 90.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 382–571 1.000 90.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 384–573 1.000 90.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 372–561 1.000 90.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 GGTTTTGCGCCAAGAATTCA TTTCCTTGAAAGGGGTGCTC 833–1444 1.000 90.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 TGGTTTTGCGCCAAGAATTC TTTCCTTGAAAGGGGTGCTC 834–1445 1.000 90.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTTCCTTGAAAGGGGTGCTC 632–1243 1.000 90.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTCCTTGAAAGGGGTGCTC 631–1242 1.000 90.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 GGTTTTGCGCCAAGAATTCA ATCCCGAAGAGATGGCAAAC 923–1534 1.000 90.5
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG AGGAATCCGAAGATGAATAGAGA 300–500 0.923 51.2
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT AGGAATCCGAAGATGAATAGAGA 297–497 0.923 49.2
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT AGGAATCCGAAGATGAATAGAGA 298–498 0.923 49.2
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT AGGAATCCGAAGATGAATAGAGA 299–499 0.923 49.2
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG AGGAATCCGAAGATGAATAGAGAA 300–500 0.923 48.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGGGCTATTAGAACGAATCACA 782–1077 1.000 75.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGGGCTATTAGAACGAATCACA 781–1076 1.000 75.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGGGGCTATTAGAACGAATCAC 783–1078 1.000 73.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AGGGGCTATTAGAACGAATCAC 782–1077 1.000 73.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC GGGGCTATTAGAACGAATCACA 784–1079 1.000 72.6
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AAATCAATTGCGTCCATGCG 523–583 0.962 89.5
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CAGCCTTCCAAGCTAACGAT AAATCAATTGCGTCCATGCG 524–584 0.962 89.5
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU CCTCAGCCTTCCAAGCTAAC AAATCAATTGCGTCCATGCG 527–587 0.962 87.7
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CTAACGATGCGGGTTCGATT AAATCAATTGCGTCCATGCG 512–572 0.962 86.3
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CGTCGACTATAACCCTCAGC AAATCAATTGCGTCCATGCG 540–600 0.923 85.0
atpH-atpI_p1 atpH-atpI CTCGCGATACCTTCTACAGC GAGTTACCTCAGGGGGAGTT 1038–1195 1.000 91.3
atpH-atpI_p2 atpH-atpI CTCGCGATACCTTCTACAGC GCGAATCCATGGAAGGTCAT 680–837 0.962 89.9
atpH-atpI_p3 atpH-atpI CTCGCGATACCTTCTACAGC TCCACAAACCATTCCCACTG 1219–1376 0.923 88.5
atpH-atpI_p4 atpH-atpI GCAGCAATAACAGAAGCAGC TCCACAAACCATTCCCACTG 1135–1292 0.923 88.1
atpH-atpI_p5 atpH-atpI ACCCGCGGAAAGAAAAGAAT TCCACAAACCATTCCCACTG 1677–1849 0.923 87.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (26)

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

Species Accession Length (bp) Link
Parnassia brevistyla NC_065698.1 151722 View on NCBI ↗
Parnassia chinensis NC_060785.1 152049 View on NCBI ↗
Parnassia crassifolia NC_065713.1 152321 View on NCBI ↗
Parnassia degeensis NC_065703.1 152161 View on NCBI ↗
Parnassia delavayi NC_061946.1 151640 View on NCBI ↗
Parnassia deqenensis NC_061940.1 152079 View on NCBI ↗
Parnassia epunctulata NC_061956.1 152167 View on NCBI ↗
Parnassia filchneri NC_065700.1 153851 View on NCBI ↗
Parnassia foliosa NC_065716.1 151256 View on NCBI ↗
Parnassia gansuensis NC_065702.1 152483 View on NCBI ↗
Parnassia leptophylla NC_061944.1 152064 View on NCBI ↗
Parnassia longipetala NC_061955.1 152028 View on NCBI ↗
Parnassia longshengensis NC_065701.1 151873 View on NCBI ↗
Parnassia lutea NC_060784.1 153152 View on NCBI ↗
Parnassia mysorensis NC_065729.1 152055 View on NCBI ↗
Parnassia noemiae NC_065718.1 152060 View on NCBI ↗
Parnassia nubicola NC_061943.1 153668 View on NCBI ↗
Parnassia pusilla NC_065697.1 151970 View on NCBI ↗
Parnassia qinghaiensis NC_061941.1 152047 View on NCBI ↗
Parnassia submysorensis NC_065699.1 152145 View on NCBI ↗
Parnassia tenella NC_060783.1 152032 View on NCBI ↗
Parnassia tibetana NC_061957.1 151637 View on NCBI ↗
Parnassia trinervis NC_043951.1 153590 View on NCBI ↗
Parnassia venusta NC_061942.1 152099 View on NCBI ↗
Parnassia viridiflora NC_060782.1 153811 View on NCBI ↗
Parnassia wightiana NC_061947.1 151704 View on NCBI ↗