Markers + reference

Chrysosplenium

33 species · Saxifragaceae · Saxifragales

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Species 33
Genome length 152–153 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
psbA LSC 1062 0.0114 1.00 52.7 yes View details
trnK-UUU-rps16 LSC 722 0.0606 0.96 80.2 yes View details
rps16-trnQ-UUG LSC 750 0.1013 0.95 83.9 yes View details
trnR-UCU-atpA LSC 248 0.0908 0.91 70.2 yes View details
trnE-UUC-trnT-GGU LSC 824 0.0666 0.93 82.4 yes View details
trnT-GGU-psbD LSC 1297 0.0419 0.98 81.5 yes View details
psbZ-trnG-GCC LSC 576 0.0853 0.86 74.2 yes View details
trnT-UGU-trnL-UAA LSC 1251 0.0949 0.74 78.1 yes View details
ndhC-trnV-UAC LSC 711 0.0554 0.95 81.7 yes View details
ndhF-rpl32 SSC 953 0.0678 0.92 77.9 yes View details
trnC-GCA-petN LSC 749 0.0427 0.98 84.5 yes View details
psaA-ycf3 LSC 618 0.0300 1.00 84.5 yes View details
psbM-trnD-GUC LSC 756 0.0456 0.98 83.7 yes View details
trnF-GAA-ndhJ LSC 495 0.0641 0.96 83.6 yes View details
rpl32-trnL-UAG SSC 489 0.0556 0.97 83.6 yes View details
trnS-GCU-trnG-UCC LSC 457 0.0590 1.00 80.8 yes View details
trnD-GUC-trnY-GUA LSC 427 0.0491 1.00 80.2 yes View details
psbE-petL LSC 1002 0.0406 0.98 80.2 yes View details
rpl20-rps12 LSC 727 0.0346 0.99 80.0 yes View details
rpoB-trnC-GCA LSC 1069 0.0430 0.97 78.6 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA CTACATCCGCCCCTACCTAA TAGTCATAGTCCCAGCGAGG 1729–1757 0.182 49.4
psbA_p2 psbA CTGCCTTAATCCACTTGGCT TAGTCATAGTCCCAGCGAGG 1747–1775 0.182 48.4
psbA_p3 psbA ACTGCCTTAATCCACTTGGC TAGTCATAGTCCCAGCGAGG 1748–1776 0.182 48.2
psbA_p4 psbA ACTTGCATACGCTAAGACCG TAGTCATAGTCCCAGCGAGG 1498 0.152 46.1
psbA_p5 psbA CTACATCCGCCCCTACCTAA AAGCCGTGTGCAATGAAAAG 1675 0.030 40.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CAGCCCAATCGCTCTTTTTG GGTCAAAAGTGTAACACGCG 1811–2104 0.879 86.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CAGCCCAATCGCTCTTTTTG GTCAAAAGTGTAACACGCGG 1810–2103 0.879 86.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CAGCCCAATCGCTCTTTTTG CGGTCAAAAGTGTAACACGC 1812–2105 0.818 84.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GGTCAAAAGTGTAACACGCG 1408–1694 0.758 82.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GTCAAAAGTGTAACACGCGG 1407–1693 0.758 82.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 435–1269 1.000 91.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCGGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 433–1267 1.000 91.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AGCGGATCATGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 434–1268 1.000 88.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GCGTTGCTTTCTACCACATC GAGGTTCGAATCCTTCCGTC 410–1244 0.970 86.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCG GAGGTTCGAATCCTTCCGTC 835–1263 0.061 51.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TACCACTAAACTATACCCGC 512–810 1.000 59.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TACCACTAAACTATACCCGC 511–809 1.000 59.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TTACCACTAAACTATACCCGC 513–811 1.000 58.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TTACCACTAAACTATACCCGC 512–810 1.000 58.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TACCACTAAACTATACCCGC 566–864 1.000 58.7
trnR-UCU-atpA_p1 trnR-UCU-atpA GCTCGGTGGAAAGAAAATGC CATTCACTGAGGAAGCGGAA 839–1018 0.515 71.7
trnR-UCU-atpA_p2 trnR-UCU-atpA TTCAAATCCTGTTGGACGCA CATTCACTGAGGAAGCGGAA 315–465 0.515 71.6
trnR-UCU-atpA_p3 trnR-UCU-atpA CCGCTACCCGCTTTATCTTT CATTCACTGAGGAAGCGGAA 503–682 0.515 71.4
trnR-UCU-atpA_p4 trnR-UCU-atpA CCTAGCCTTCCAAGCTAACG CATTCACTGAGGAAGCGGAA 538–717 0.515 71.3
trnR-UCU-atpA_p5 trnR-UCU-atpA TCGGTCACGTCTTAGATCGA CATTCACTGAGGAAGCGGAA 664–772 0.212 57.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCCCACCTACACAAGCAAAT CCGGATTTGAACTGGGGAAA 1301–1991 0.970 89.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCCCACCTACACAAGCAAAT CAATTAGATTCCCCGTCCGG 1445–2135 0.758 80.7
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCCCACCTACACAAGCAAAT CCAATTAGATTCCCCGTCCG 1446–2091 0.606 74.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCTTGCATATCCCTACCGGT CCGGATTTGAACTGGGGAAA 1382–1527 0.455 68.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCTTGCATATCCCTACCGGT CAATTAGATTCCCCGTCCGG 1527–1671 0.394 65.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (33)

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

Species Accession Length (bp) Link
Chrysosplenium album NC_067019.1 153066 View on NCBI ↗
Chrysosplenium alternifolium NC_051986.1 152619 View on NCBI ↗
Chrysosplenium aureobracteatum NC_039740.1 153102 View on NCBI ↗
Chrysosplenium axillare NC_067016.1 152089 View on NCBI ↗
Chrysosplenium delavayi NC_067004.1 153484 View on NCBI ↗
Chrysosplenium echinus NC_067020.1 152375 View on NCBI ↗
Chrysosplenium fallax NC_084262.1 152527 View on NCBI ↗
Chrysosplenium fauriei NC_067023.1 152221 View on NCBI ↗
Chrysosplenium forrestii NC_067027.1 151961 View on NCBI ↗
Chrysosplenium giraldianum NC_067011.1 153249 View on NCBI ↗
Chrysosplenium glossophyllum NC_067008.1 152325 View on NCBI ↗
Chrysosplenium grayanum NC_067018.1 152565 View on NCBI ↗
Chrysosplenium griffithii NC_067010.1 152364 View on NCBI ↗
Chrysosplenium griffithii var. intermedium OK336543.1 152349 View on NCBI ↗
Chrysosplenium henryi NC_066997.1 152350 View on NCBI ↗
Chrysosplenium hydrocotylifolium NC_067005.1 152228 View on NCBI ↗
Chrysosplenium kamtschaticum NC_051988.1 152561 View on NCBI ↗
Chrysosplenium kiotense NC_067021.1 152866 View on NCBI ↗
Chrysosplenium lectus-cochleae NC_067013.1 152500 View on NCBI ↗
Chrysosplenium macrophyllum MK973001.3 152837 View on NCBI ↗
Chrysosplenium macrostemon NC_067022.1 152173 View on NCBI ↗
Chrysosplenium nepalense NC_067000.1 153475 View on NCBI ↗
Chrysosplenium nudicaule MZ424445.1 152775 View on NCBI ↗
Chrysosplenium pilosum NC_067001.1 152676 View on NCBI ↗
Chrysosplenium ramosum MK973002.2 153460 View on NCBI ↗
Chrysosplenium sinicum NC_051987.1 153427 View on NCBI ↗
Chrysosplenium taibaishanense NC_067015.1 152347 View on NCBI ↗
Chrysosplenium tetrandrum NC_084132.1 152934 View on NCBI ↗
Chrysosplenium uniflorum NC_066998.1 151702 View on NCBI ↗
Chrysosplenium valdepilosum NC_084135.1 152676 View on NCBI ↗
Chrysosplenium valdivicum NC_084134.1 151607 View on NCBI ↗
Chrysosplenium wrightii NC_084133.1 153139 View on NCBI ↗
Chrysosplenium zhouzhiense NC_067014.1 151855 View on NCBI ↗