Markers + reference

Philadelphus

2 species · Hydrangeaceae · Cornales

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Species 2
Genome length 157–158 kb
Candidate markers 270
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 35.1 yes View details
rps16-trnQ-UUG LSC 1657 0.0024 1.00 48.3 yes View details
atpH-atpI LSC 1125 0.0027 1.00 60.4 yes View details
trnC-GCA-petN LSC 834 0.0072 1.00 62.9 yes View details
ndhC-trnV-UAC LSC 1166 0.0052 0.99 62.4 yes View details
rps18-rpl20 LSC 302 0.0066 1.00 42.2 yes View details
rpl14 LSC 369 0.0000 1.00 23.8 yes View details
ycf1 IRb 962 0.0010 1.00 48.6 no View details
ndhD SSC 1503 0.0007 1.00 48.9 yes View details
ndhA SSC 2199 0.0023 1.00 58.1 yes View details
ycf1 SSC 5679 0.0026 1.00 43.3 yes View details
rpl14-rpl16 LSC 139 0.0146 0.99 62.3 yes View details
matK-trnK-UUU LSC 702 0.0057 1.00 62.0 yes View details
ccsA-ndhD SSC 245 0.0163 1.00 61.9 yes View details
trnT-UGU-trnL-UAA LSC 665 0.0045 1.00 61.3 yes View details
rpl32-trnL-UAG SSC 861 0.0035 1.00 60.9 yes View details
rps4-trnT-UGU LSC 395 0.0027 0.95 60.7 yes View details
atpB-rbcL LSC 749 0.0027 1.00 60.7 yes View details
psbA-trnK-UUU LSC 215 0.0140 1.00 60.5 yes View details
trnQ-UUG LSC 72 0.0139 1.00 60.5 yes View details
trnS-GCU-trnG-UCC LSC 809 0.0000 0.98 60.4 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA GCAATACCGCCCTCTTGATA ATTTGTGTGCTTGGGAGTCC 1199 1.000 72.6
psbA_p2 psbA AAAAAGGAGCAATACCGCCC ATTTGTGTGCTTGGGAGTCC 1207 1.000 70.4
psbA_p3 psbA ACCGCCCTCTTGATAAAACA ATTTGTGTGCTTGGGAGTCC 1194 1.000 70.0
psbA_p4 psbA AAAAGGAGCAATACCGCCC ATTTGTGTGCTTGGGAGTCC 1206 1.000 68.0
psbA_p5 psbA ACCGCCCTCTTGATAAAACAA ATTTGTGTGCTTGGGAGTCC 1194 1.000 67.8
psbA-trnK-UUU_p1 psbA-trnK-UUU CAATTACAGAAGCGACCCCA GAAAGCCGTGTGCAATGAAA 390 1.000 78.7
psbA-trnK-UUU_p2 psbA-trnK-UUU CAATTACAGAAGCGACCCCA CGGCTTGGGGAGAGATTTTT 360 1.000 78.5
psbA-trnK-UUU_p3 psbA-trnK-UUU CAATTACAGAAGCGACCCCA CTAGTTCCGGGTTCGAATCC 305 1.000 78.2
psbA-trnK-UUU_p4 psbA-trnK-UUU ACGGTTTTCAGTGCTGGTTA GAAAGCCGTGTGCAATGAAA 412 1.000 76.8
psbA-trnK-UUU_p5 psbA-trnK-UUU ACGGTTTTCAGTGCTGGTTA CGGCTTGGGGAGAGATTTTT 382 1.000 76.7
trnK-UUU_p1 trnK-UUU CATATACATATGATTTCGATATGACA TCAATGCTTTGATTTCCTCGT 2645 1.000 40.2
trnK-UUU_p2 trnK-UUU CATATACATATGATTTCGATATGACA AGTTCAATGCTTTGATTTCCTCG 2648 1.000 40.2
trnK-UUU_p3 trnK-UUU CATATACATATGATTTCGATATGACA TTCAATGCTTTGATTTCCTCGT 2646 1.000 40.2
trnK-UUU_p4 trnK-UUU CATATACATATGATTTCGATATGACAA TCAATGCTTTGATTTCCTCGT 2645 1.000 40.2
trnK-UUU_p5 trnK-UUU CATATACATATGATTTCGATATGACA GTTCAATGCTTTGATTTCCTCGT 2647 1.000 40.2
matK-trnK-UUU_p1 matK-trnK-UUU CCATGATCATGAGCAAGTGC AACGGTAGAGTACTCGGCTT 833 1.000 72.8
matK-trnK-UUU_p2 matK-trnK-UUU CCATGATCATGAGCAAGTGC ACGGTAGAGTACTCGGCTTT 832 1.000 72.8
matK-trnK-UUU_p3 matK-trnK-UUU CCATGATCATGAGCAAGTGC GGGTTGCTAACTCAACGGTA 846 1.000 70.5
matK-trnK-UUU_p4 matK-trnK-UUU AGGAAGTCGTGTTGCTGATA AACGGTAGAGTACTCGGCTT 782 1.000 67.7
matK-trnK-UUU_p5 matK-trnK-UUU AGGAAGTCGTGTTGCTGATA ACGGTAGAGTACTCGGCTTT 781 1.000 67.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1747 1.000 78.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1730 1.000 78.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1748 1.000 77.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1745 1.000 76.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1744 1.000 76.6
trnQ-UUG_p1 trnQ-UUG TCCAAAACACAATCTTGATTCTGA GGTTGGAATTGACGAAAAACCA 175 1.000 40.5
trnQ-UUG_p2 trnQ-UUG TCCAAAACACAATCTTGATTCTGA TGGGTTGGAATTGACGAAAAAC 177 1.000 40.5
trnQ-UUG_p3 trnQ-UUG TCCAAAACACAATCTTGATTCTGA TGGGTTGGAATTGACGAAAA 177 1.000 40.5
trnQ-UUG_p4 trnQ-UUG TCCAAAACACAATCTTGATTCTGA TTGGGTTGGAATTGACGAAA 178 1.000 40.4
trnQ-UUG_p5 trnQ-UUG TCCAAAACACAATCTTGATTCTGA TTTGGGTTGGAATTGACGAA 179 1.000 40.4

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
Philadelphus calvescens NC_044779.1 157515 View on NCBI ↗
Philadelphus pekinensis NC_060600.1 157308 View on NCBI ↗