Markers + reference

Mukdenia

2 species · Saxifragaceae · Saxifragales

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Species 2
Genome length 157–157 kb
Candidate markers 269
Primer pairs 95

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 8 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 332 0.0457 0.99 80.6 yes View details
trnC-GCA-petN LSC 858 0.0072 0.98 65.1 yes View details
petN-psbM LSC 668 0.0195 1.00 68.9 yes View details
psbC-trnS-UGA LSC 246 0.0285 1.00 61.4 yes View details
petA-psbJ LSC 731 0.0069 1.00 48.8 yes View details
ycf1 IRb 1201 0.0017 1.00 44.7 no View details
ndhF SSC 2247 0.0031 1.00 45.6 yes View details
ccsA SSC 957 0.0042 1.00 50.1 yes View details
ndhD SSC 1503 0.0033 1.00 47.4 yes View details
ycf1 SSC 5625 0.0021 1.00 53.9 yes View details
trnM-CAU-atpE LSC 169 0.0536 0.99 77.0 yes View details
psbT-psbN LSC 60 0.0333 1.00 71.7 yes View details
rps16-trnQ-UUG LSC 1688 0.0043 0.95 65.3 yes View details
ndhI-ndhA SSC 76 0.0139 0.95 65.2 yes View details
ycf1-ndhF SSC 22 0.0455 1.00 65.1 yes View details
trnK-UUU-rps16 LSC 622 0.0048 1.00 61.7 yes View details
trnT-UGU-trnL-UAA LSC 1069 0.0038 0.99 61.6 yes View details
atpF LSC 1299 0.0031 0.99 61.5 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 95 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 394–398 1.000 82.3
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 397–401 1.000 82.2
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 408–412 1.000 82.1
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 407–411 1.000 82.1
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 409–413 1.000 82.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA AAAAAGGCGCTCAACCTACA 799–805 1.000 79.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC AAAAAGGCGCTCAACCTACA 800–806 1.000 79.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 ATGGACGAATCCCTTGCTTC AAAAAGGCGCTCAACCTACA 804–810 1.000 79.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT AAAAAGGCGCTCAACCTACA 802–808 1.000 79.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT AAAAAGGCGCTCAACCTACA 833–839 1.000 79.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATCAAAATGGGGCGTGG 1746–1819 1.000 82.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1688–1761 1.000 82.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAAATCAAAATGGGGCGTGG 1757–1830 1.000 82.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1699–1772 1.000 81.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAAATCAAAATGGGGCGTGG 1767–1840 1.000 80.3
trnG-GCC_p1 trnG-GCC TCCCCCAACAAAACATGTCA TGTGTATTCAATTCAACGATGCA 946–947 1.000 47.8
trnG-GCC_p2 trnG-GCC AGTCCCCCAACAAAACATGT TGTGTATTCAATTCAACGATGCA 948–949 1.000 47.7
trnG-GCC_p3 trnG-GCC GTCCCCCAACAAAACATGTC TGTGTATTCAATTCAACGATGCA 947–948 1.000 45.0
trnG-GCC_p4 trnG-GCC TCCCCCAACAAAACATGTCA TTGTGTATTCAATTCAACGATGCA 947–948 1.000 44.7
trnG-GCC_p5 trnG-GCC AGTCCCCCAACAAAACATGT TTGTGTATTCAATTCAACGATGCA 949–950 1.000 44.6
atpF_p1 atpF GCTCGAATGGTTACCATGAGT GGGGGCGAAGTGATACAAAA 1432–1445 1.000 70.8
atpF_p2 atpF CAGCTCGAATGGTTACCATGA GGGGGCGAAGTGATACAAAA 1434–1447 1.000 70.8
atpF_p3 atpF CATCAGCTCGAATGGTTACCA GGGGGCGAAGTGATACAAAA 1437–1450 1.000 70.8
atpF_p4 atpF TCAGCTCGAATGGTTACCATG GGGGGCGAAGTGATACAAAA 1435–1448 1.000 70.8
atpF_p5 atpF GCTCGATACGTTCCCGGATA GGGGGCGAAGTGATACAAAA 1470–1483 1.000 70.6
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 914–919 1.000 80.4
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 975–980 1.000 78.7
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 932–937 1.000 78.2
trnC-GCA-petN_p4 trnC-GCA-petN ATTTTGGATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 971–976 1.000 78.0
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGAGTCCACTTCTTCCCCAT 993–998 1.000 76.4

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
Mukdenia acanthifolia NC_062439.1 156935 View on NCBI ↗
Mukdenia rossii NC_037495.1 156960 View on NCBI ↗