Markers + reference

Loropetalum

2 species · Hamamelidaceae · Saxifragales

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Species 2
Genome length 159–159 kb
Candidate markers 269
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 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 379 0.0026 1.00 55.7 yes View details
atpA LSC 1524 0.0007 1.00 59.1 yes View details
atpH-atpI LSC 1143 0.0009 1.00 59.3 yes View details
atpI LSC 744 0.0013 1.00 59.5 yes View details
psbM-trnD-GUC LSC 1133 0.0000 1.00 35.6 yes View details
trnD-GUC-trnY-GUA LSC 426 0.0023 1.00 56.5 yes View details
ndhC-trnV-UAC LSC 1214 0.0008 1.00 59.2 yes View details
atpB-rbcL LSC 703 0.0028 1.00 60.4 yes View details
rbcL-accD LSC 623 0.0000 1.00 58.9 yes View details
ycf1 IRb 1002 0.0000 1.00 40.0 no View details
ycf1 SSC 5565 0.0004 1.00 52.7 yes View details
trnF-GAA-ndhJ LSC 713 0.0000 0.99 60.0 yes View details
trnR-ACG-trnN-GUU IRb 589 0.0017 1.00 59.5 yes View details
trnN-GUU-trnR-ACG IRa 589 0.0017 1.00 59.5 yes View details
accD LSC 1503 0.0007 1.00 59.1 yes View details
petB LSC 1441 0.0007 1.00 59.1 yes View details
ndhD SSC 1521 0.0007 1.00 59.1 yes View details
matK-trnK-UUU LSC 703 0.0000 1.00 59.0 yes View details
rps16-trnQ-UUG LSC 1661 0.0000 1.00 58.5 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 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 ATGCATGAACGTAACGCTCA 473 1.000 76.9
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TGCATGAACGTAACGCTCAT 472 1.000 76.9
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA ATGCATGAACGTAACGCTCA 487 1.000 76.9
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TGCATGAACGTAACGCTCAT 486 1.000 76.9
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TGCATGAACGTAACGCTCAT 485 1.000 76.9
trnK-UUU_p1 trnK-UUU TGTGAATGGATGAAGTGAGT TGGTTTGATTGCGTCGTACA 2688–2690 1.000 49.2
trnK-UUU_p2 trnK-UUU TGTGAATGGATGAAGTGAGTT TGGTTTGATTGCGTCGTACA 2688–2690 1.000 48.1
trnK-UUU_p3 trnK-UUU TTGTGAATGGATGAAGTGAGT TGGTTTGATTGCGTCGTACA 2689–2691 1.000 48.1
trnK-UUU_p4 trnK-UUU TGTGAATGGATGAAGTGAGT TTGCGTCGTACAATCCAGTC 2680–2682 1.000 47.9
trnK-UUU_p5 trnK-UUU TGTGAATGGATGAAGTGAGT CAATGGTTTGATTGCGTCGT 2691–2693 1.000 47.6
matK-trnK-UUU_p1 matK-trnK-UUU GGAAGTCATGTTGCCGAGAT AACGGTAGAGTACTCGGCTT 780–782 1.000 78.6
matK-trnK-UUU_p2 matK-trnK-UUU GGAAGTCATGTTGCCGAGAT ACGGTAGAGTACTCGGCTTT 779–781 1.000 78.6
matK-trnK-UUU_p3 matK-trnK-UUU GGAAGTCATGTTGCCGAGAT TTGCGTCGTACAATCCAGTC 872–874 1.000 77.6
matK-trnK-UUU_p4 matK-trnK-UUU GGAAGTCATGTTGCCGAGAT ATTGCGTCGTACAATCCAGT 873–875 1.000 76.9
matK-trnK-UUU_p5 matK-trnK-UUU GGAAGTCATGTTGCCGAGAT TTGGGTTGCTAACTCAACGG 795–797 1.000 76.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 1740–1741 1.000 79.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG TACAAATCGAAATGGGGCGT 1800–1801 1.000 79.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 1742–1743 1.000 78.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1733–1734 1.000 78.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT TACAAATCGAAATGGGGCGT 1802–1803 1.000 78.0
trnG-GCC_p1 trnG-GCC CCTGTCTTGATTACGTCCGG GAGAATTTCGGGAATTGCGT 909–910 1.000 69.8
trnG-GCC_p2 trnG-GCC CCGACAAAACACGTCAACAG GAGAATTTCGGGAATTGCGT 955–956 1.000 69.8
trnG-GCC_p3 trnG-GCC TAAGTCCCCGACAAAACACG GAGAATTTCGGGAATTGCGT 962–963 1.000 69.4
trnG-GCC_p4 trnG-GCC TACGTCCGGTTCCTTTGTTC GAGAATTTCGGGAATTGCGT 898–899 1.000 69.2
trnG-GCC_p5 trnG-GCC CCTGTCTTGATTACGTCCGG AGAGAATTTCGGGAATTGCGT 910–911 1.000 69.2
atpA_p1 atpA TGATTTGAATCAGACACACTTCT TGTTTGGGGCGATGAAAGAA 1726 1.000 41.0
atpA_p2 atpA TGATTTGAATCAGACACACTTCT ATGTTTGGGGCGATGAAAGA 1727 1.000 40.0
atpA_p3 atpA TGATTTGAATCAGACACACTTCT GGTATGTTTGGGGCGATGAA 1730 1.000 40.0
atpA_p4 atpA TGATTTGAATCAGACACACTTC TGTTTGGGGCGATGAAAGAA 1726 1.000 40.0
atpA_p5 atpA TGATTTGAATCAGACACACTTCT ATTGGTATGTTTGGGGCGAT 1733 1.000 40.0

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
Loropetalum chinense NC_060831.1 159444 View on NCBI ↗
Loropetalum chinense var. rubrum ON729351.1 159439 View on NCBI ↗