Markers + reference

Saururus

2 species · Saururaceae · Piperales

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Species 2
Genome length 161–162 kb
Candidate markers 274
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 IRb 1431 0.0007 1.00 46.8 no View details
ndhF SSC 2220 0.4649 0.78 77.5 yes View details
ccsA SSC 972 0.4908 0.90 82.1 yes View details
ccsA-ndhD SSC 273 0.4683 0.92 76.6 yes View details
ndhD SSC 1506 0.4867 0.82 80.0 yes View details
ndhA SSC 2201 0.4688 0.87 79.9 yes View details
ndhH SSC 1182 0.5021 0.80 79.4 yes View details
ycf1 SSC 5502 0.3261 0.88 75.5 yes View details
ndhF IRa 12 0.0000 1.00 18.9 no View details
psbT-psbN LSC 63 0.0794 1.00 81.8 yes View details
ndhF-rpl32 SSC 1266 0.4575 0.82 80.0 yes View details
ndhI SSC 513 0.4459 0.87 79.6 yes View details
ndhG-ndhI SSC 401 0.4395 0.95 79.4 yes View details
rpl32-trnL-UAG SSC 1115 0.4276 0.76 78.1 yes View details
rps15-ycf1 SSC 379 0.3952 0.88 77.1 yes View details
rpl32 SSC 174 0.4601 0.94 77.0 yes View details
trnL-UAG-ccsA SSC 128 0.4636 0.86 76.1 yes View details
ndhG SSC 531 0.4293 0.71 75.4 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbT-psbN_p1 psbT-psbN CGCCTAGGATTTCGACGAAA AGATCCGTTCGAAGAACACG 123 1.000 82.4
psbT-psbN_p2 psbT-psbN CGCCTAGGATTTCGACGAAA TCGCCATCTCCATATCTGGT 208 1.000 81.1
psbT-psbN_p3 psbT-psbN CGCCTAGGATTTCGACGAAA CCCTAGTCGCCATCTCCATA 214 1.000 80.6
psbT-psbN_p4 psbT-psbN CGAGAACCGCCTAGGATTTC TCGCCATCTCCATATCTGGT 215 1.000 80.6
psbT-psbN_p5 psbT-psbN GAGAACCGCCTAGGATTTCG TCGCCATCTCCATATCTGGT 214 1.000 80.6
ndhF_p1 ndhF CCGATTGTGCCATGATGAGA CCGTTGGGTAGAGTTTTCGT 2798 0.500 58.4
ndhF_p2 ndhF TCCGATTGTGCCATGATGAG CCGTTGGGTAGAGTTTTCGT 2799 0.500 58.4
ndhF_p3 ndhF CAGAAAAAGGATCCCCGGAG CCGTTGGGTAGAGTTTTCGT 2943 0.500 58.4
ndhF_p4 ndhF GGATCCGATTGTGCCATGAT CCGTTGGGTAGAGTTTTCGT 2802 0.500 57.9
ndhF_p5 ndhF GACAGAAAAAGGATCCCCGG CCGTTGGGTAGAGTTTTCGT 2945 0.500 56.7
ndhF-rpl32_p1 ndhF-rpl32 AGTAACTGGGAGTGGAACGA TGCCGCCCAATATCCTTTTT 1407 0.500 58.8
ndhF-rpl32_p2 ndhF-rpl32 AGTAACTGGGAGTGGAACGA TTGCCGCCCAATATCCTTTT 1408 0.500 58.8
ndhF-rpl32_p3 ndhF-rpl32 AGTAACTGGGAGTGGAACGA TTTGCCGCCCAATATCCTTT 1409 0.500 58.8
ndhF-rpl32_p4 ndhF-rpl32 AGTAACTGGGAGTGGAACGA TTTTGCCGCCCAATATCCTT 1410 0.500 58.8
ndhF-rpl32_p5 ndhF-rpl32 AGTAACTGGGAGTGGAACGA TTTTTGCCGCCCAATATCCT 1411 0.500 58.8
rpl32_p1 rpl32 TGAGGTGGAGGACGAATTCT GGAACAGATCCGTGGTATGG 965 0.500 57.6
rpl32_p2 rpl32 TGAGGTGGAGGACGAATTCT TCGAGTCATGTCAATTGCGA 488 0.500 56.6
rpl32_p3 rpl32 TACTCTATCCTCGGGAGTGC GGAACAGATCCGTGGTATGG 1221 0.500 55.9
rpl32_p4 rpl32 CTCTATCCTCGGGAGTGCTT GGAACAGATCCGTGGTATGG 1219 0.500 55.7
rpl32_p5 rpl32 TACTCTATCCTCGGGAGTGC TCGAGTCATGTCAATTGCGA 744 0.500 54.9
rpl32-trnL-UAG_p1 rpl32-trnL-UAG TGAGGTGGAGGACGAATTCT TTGGGGCTGTAATTGCACTT 2104 0.500 59.4
rpl32-trnL-UAG_p2 rpl32-trnL-UAG TGAGGTGGAGGACGAATTCT TCGTGCCCTTTTCTAACGAG 1927 0.500 58.9
rpl32-trnL-UAG_p3 rpl32-trnL-UAG TGAGGTGGAGGACGAATTCT AGAAGTAGCTATCGTGCCCT 1938 0.500 58.9
rpl32-trnL-UAG_p4 rpl32-trnL-UAG AAGGATATTGGGCGGCAAAA TTGGGGCTGTAATTGCACTT 1743 0.500 58.8
rpl32-trnL-UAG_p5 rpl32-trnL-UAG AGGATATTGGGCGGCAAAAA TTGGGGCTGTAATTGCACTT 1742 0.500 58.8
trnL-UAG-ccsA_p1 trnL-UAG-ccsA GCCTAATCGTCCCGGATTTT TTGGGGCTGTAATTGCACTT 730 0.500 59.6
trnL-UAG-ccsA_p2 trnL-UAG-ccsA GCCTAATCGTCCCGGATTTT TACTGTACCCCGCCAAGTAA 992 0.500 59.2
trnL-UAG-ccsA_p3 trnL-UAG-ccsA GCCTAATCGTCCCGGATTTT TCGTGCCCTTTTCTAACGAG 553 0.500 59.1
trnL-UAG-ccsA_p4 trnL-UAG-ccsA GCCTAATCGTCCCGGATTTT AGAAGTAGCTATCGTGCCCT 564 0.500 59.1
trnL-UAG-ccsA_p5 trnL-UAG-ccsA TAGACACGCTGCTCTTAGGA TTGGGGCTGTAATTGCACTT 502 0.500 58.9

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
Saururus cernuus NC_087887.1 161811 View on NCBI ↗
Saururus chinensis NC_050853.1 161489 View on NCBI ↗