Markers + reference

Heuchera

12 species · Saxifragaceae · Saxifragales

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Species 12
Genome length 155–156 kb
Candidate markers 270
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1352 0.0122 0.99 61.1 yes View details
trnR-UCU-atpA LSC 216 0.0255 0.93 56.9 yes View details
psbZ-trnG-UCC LSC 478 0.0312 0.98 75.9 yes View details
trnT-trnL-UAA LSC 985 0.0141 0.88 55.0 yes View details
trnF-GAA-ndhJ LSC 649 0.0114 0.99 55.3 yes View details
petA-psbJ LSC 730 0.0099 0.99 63.5 yes View details
rpl20 LSC 387 0.0054 1.00 34.1 yes View details
ycf1 IRb 1289 0.0009 1.00 41.2 no View details
ndhF SSC 2244 0.0060 0.99 40.5 yes View details
ndhD SSC 1503 0.0068 1.00 38.4 yes View details
ycf1 SSC 5631 0.0067 0.99 46.8 yes View details
ycf1 IRa 1289 0.0006 1.00 28.4 no View details
ndhC-trnV-UAC LSC 1092 0.0088 1.00 66.3 yes View details
ccsA-ndhD SSC 223 0.0341 0.96 58.6 yes View details
rps19-trnH-GUG LSC 10 0.0909 1.00 58.3 yes View details
trnP-UGG-psaJ LSC 404 0.0068 1.00 57.0 yes View details
rpoB-trnC-GCA LSC 1222 0.0068 1.00 54.9 yes View details
trnN-GUU-trnR-ACG IRa 601 0.0053 0.99 54.9 yes View details
petN-psbM LSC 699 0.0099 0.97 54.5 yes View details
trnR-ACG-trnN-GUU IRb 601 0.0037 0.99 53.7 yes View details
atpB-rbcL LSC 764 0.0050 0.97 53.5 yes View details
atpA-atpF LSC 66 0.0175 0.97 53.2 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 999–1741 1.000 84.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1010–1752 1.000 84.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1020–1762 1.000 82.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 1021–1763 1.000 82.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AGAAAGCTAAATGGGGCGTG 1058–1800 1.000 80.9
trnR-UCU-atpA_p1 trnR-UCU-atpA ATGAAAGGCGTCCATTGTCT GAGGAAGCAGAAGCCCTTTT 343–370 1.000 82.9
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAGGCGTCCATTG GAGGAAGCAGAAGCCCTTTT 346–373 1.000 82.3
trnR-UCU-atpA_p3 trnR-UCU-atpA ATGAAAGGCGTCCATTGTCT AGGAAGCAGAAGCCCTTTTG 342–369 0.917 77.0
trnR-UCU-atpA_p4 trnR-UCU-atpA ATGAAAGGCGTCCATTGTCT GGAAGCAGAAGCCCTTTTGA 341–368 0.917 77.0
trnR-UCU-atpA_p5 trnR-UCU-atpA GGAATGAAAGGCGTCCATTG AGGAAGCAGAAGCCCTTTTG 345–372 0.917 76.5
atpA-atpF_p1 atpA-atpF ATGCCATCGCCTACTTGAAG TGTTTGGGGCGATGAAAGAA 209–214 1.000 82.6
atpA-atpF_p2 atpA-atpF ATTGCTCAATACGTTCCCGG TGTTTGGGGCGATGAAAGAA 151–156 1.000 81.4
atpA-atpF_p3 atpA-atpF ATGCCATCGCCTACTTGAAG ATGTTTGGGGCGATGAAAGA 210–215 1.000 81.0
atpA-atpF_p4 atpA-atpF ATGCCATCGCCTACTTGAAG GGTATGTTTGGGGCGATGAA 213–218 1.000 80.7
atpA-atpF_p5 atpA-atpF CAATGCCATCGCCTACTTGA TGTTTGGGGCGATGAAAGAA 211–216 1.000 80.2
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AAAGTTCTTCCGTCAAGCCC CCGGATTTGAACTGGGGAAA 1386–1404 1.000 78.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCCCTCATTTCCATTCCGGA CCGGATTTGAACTGGGGAAA 1304–1322 1.000 78.4
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TTCCCTCATTTCCATTCCGG CCGGATTTGAACTGGGGAAA 1305–1323 1.000 78.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCGTCAAGCCCTGATCAATA CCGGATTTGAACTGGGGAAA 1377–1395 1.000 76.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AAAGTTCTTCCGTCAAGCCC AAAAGGATTTGCAGTCCCCC 1368–1386 1.000 76.3
petN-psbM_p1 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 702–803 1.000 72.0
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTC 702–803 1.000 67.9
petN-psbM_p3 petN-psbM TGGGGAAGAAGTGGACTCTA TGCTACTGCACTGTTCATTCT 701–802 1.000 66.7
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT GCTACTGCACTGTTCATTCT 701–802 1.000 65.5
petN-psbM_p5 petN-psbM AGTATGGGGAAGAAGTGGACT TGCTACTGCACTGTTCATTCT 705–806 1.000 65.2
psbZ-trnG-UCC_p1 psbZ-trnG-UCC TTTGCTTCTCCTGACGGTTG CGTCTTCTCCTTGGCAAAGA 605–879 1.000 83.9
psbZ-trnG-UCC_p2 psbZ-trnG-UCC ATTTGCTTCTCCTGACGGTT CGTCTTCTCCTTGGCAAAGA 606–880 1.000 82.6
psbZ-trnG-UCC_p3 psbZ-trnG-UCC GTATTTGCTTCTCCTGACGGT CGTCTTCTCCTTGGCAAAGA 608–882 1.000 78.9
psbZ-trnG-UCC_p4 psbZ-trnG-UCC TGTATTTGCTTCTCCTGACGG CGTCTTCTCCTTGGCAAAGA 609–883 1.000 78.9
psbZ-trnG-UCC_p5 psbZ-trnG-UCC CCCGTTGTATTTGCTTCTCC CGTCTTCTCCTTGGCAAAGA 614–888 1.000 77.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Heuchera abramsii MN496062.1 155527 View on NCBI ↗
Heuchera alba MN496063.1 155360 View on NCBI ↗
Heuchera caespitosa MN496064.1 155520 View on NCBI ↗
Heuchera eastwoodiae MN496065.1 155174 View on NCBI ↗
Heuchera grossulariifolia var. grossulariifolia MN496066.1 155493 View on NCBI ↗
Heuchera longipetala var. longipetala MN496067.1 155418 View on NCBI ↗
Heuchera mexicana MN496068.1 155451 View on NCBI ↗
Heuchera micrantha NC_061175.1 155469 View on NCBI ↗
Heuchera parviflora var. saurensis KR478645.1 154696 View on NCBI ↗
Heuchera parvifolia var. utahensis MN496069.1 155350 View on NCBI ↗
Heuchera richardsonii NC_042923.1 155330 View on NCBI ↗
Heuchera villosa NC_042924.1 155361 View on NCBI ↗