Markers + reference

Deutzia

11 species · Hydrangeaceae · Cornales

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Species 11
Genome length 157–157 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 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 352 0.0105 1.00 51.2 yes View details
trnK-UUU-rps16 LSC 820 0.0066 1.00 63.0 yes View details
rps16-trnQ-UUG LSC 1609 0.0053 1.00 54.1 yes View details
trnS-GCU-trnG-UCC LSC 763 0.0048 1.00 54.6 yes View details
rpoC2 LSC 4164 0.0040 1.00 49.4 yes View details
ycf3 LSC 1966 0.0017 1.00 36.2 yes View details
trnL-UAA-trnF-GAA LSC 373 0.0071 1.00 42.1 yes View details
ycf4-cemA LSC 851 0.0058 1.00 61.5 yes View details
ycf1 IRb 947 0.0000 1.00 33.5 no View details
ndhF-rpl32 SSC 1151 0.0056 1.00 55.4 yes View details
rpl32-trnL-UAG SSC 922 0.0084 1.00 56.1 yes View details
ycf1 SSC 5670 0.0031 1.00 41.7 yes View details
rpl2-trnH-GUG IRa 44 0.0244 1.00 63.8 no View details
atpB-rbcL LSC 757 0.0035 1.00 59.7 yes View details
trnG-UCC-trnR-UCU LSC 118 0.0310 1.00 57.6 yes View details
rpoB-trnC-GCA LSC 1211 0.0039 1.00 56.6 yes View details
trnF-GAA-ndhJ LSC 671 0.0054 1.00 56.1 yes View details
atpH-atpI LSC 904 0.0040 1.00 55.3 yes View details
matK LSC 1518 0.0028 1.00 54.7 yes View details
ccsA-ndhD SSC 251 0.0104 1.00 54.6 yes View details
ndhC-trnV-UAC LSC 1115 0.0036 1.00 54.3 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 TTCCCTCTAGATCTAGCGGC 414–442 1.000 85.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGATCTAGCGGC 428–456 1.000 85.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGATCTAGCGGC 427–455 1.000 85.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGATCTAGCGGC 429–457 1.000 85.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 463–491 1.000 83.7
matK_p1 matK TCGTTCCGATTAGTTAGGGA ACCCCCAAAATCCTCTACCT 1603–1612 1.000 57.2
matK_p2 matK ATCGTTCCGATTAGTTAGGGA ACCCCCAAAATCCTCTACCT 1604–1613 1.000 53.8
matK_p3 matK TCGTTCCGATTAGTTAGGGAT ACCCCCAAAATCCTCTACCT 1603–1612 1.000 53.8
matK_p4 matK TCGTTCCGATTAGTTAGGGA AACCCCCAAAATCCTCTACC 1604–1613 1.000 50.5
matK_p5 matK ATCGTTCCGATTAGTTAGGGAT ACCCCCAAAATCCTCTACCT 1604–1613 1.000 50.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCCTCGCTTCATCAA AAAAAGGCGCTCAACCTACA 997–1029 1.000 82.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AAAAAGGCGCTCAACCTACA 1010–1042 1.000 81.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGATGGTATGGACGAATCCC AAAAAGGCGCTCAACCTACA 1009–1041 1.000 81.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGAATCCCTCGCTTCATCAA AGAAGGCGGAGGTTTTCAAG 955–987 1.000 81.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGATGGTATGGACGAATCCC AGAAGGCGGAGGTTTTCAAG 967–999 1.000 81.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1699–1744 1.000 80.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1682–1727 1.000 80.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1700–1745 1.000 79.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1697–1742 1.000 78.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1696–1741 1.000 78.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AATCCAAACCGAAAGACCCC 874–897 1.000 81.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AATCCAAACCGAAAGACCCC 873–896 1.000 80.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AATCCAAACCGAAAGACCCC 928–951 1.000 79.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC AATCCAAACCGAAAGACCCC 876–899 1.000 78.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGACGCTTTAGTCCACTCAG AATCCAAACCGAAAGACCCC 869–892 1.000 78.0
trnG-UCC_p1 trnG-UCC CTTTATATACAATAATCGCATTGTG AAGAATCGGATTATATGTGAGA 858 0.091 3.6
trnG-UCC_p2 trnG-UCC CTTTATATACAATAATCGCATTGTG AAAGAATCGGATTATATGTGAGA 859 0.091 3.6
trnG-UCC_p3 trnG-UCC CTTTATATACAATAATCGCATTGTG AGAATCGGATTATATGTGAGAT 857 0.091 3.6
trnG-UCC_p4 trnG-UCC CTTTATATACAATAATCGCATTGTG AAAAGAATCGGATTATATGTGAGA 860 0.091 3.6
trnG-UCC_p5 trnG-UCC CTTTATATACAATAATCGCATTGTG AAGAATCGGATTATATGTGAGAT 858 0.091 3.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Deutzia compacta NC_044843.1 156817 View on NCBI ↗
Deutzia crassifolia MG524993.1 157035 View on NCBI ↗
Deutzia glabrata NC_057286.1 157283 View on NCBI ↗
Deutzia grandiflora NC_082968.1 157025 View on NCBI ↗
Deutzia hamata NC_082965.1 157021 View on NCBI ↗
Deutzia hypoglauca NC_082966.1 156860 View on NCBI ↗
Deutzia longifolia NC_071818.1 156942 View on NCBI ↗
Deutzia paniculata NC_084222.1 157072 View on NCBI ↗
Deutzia parviflora NC_082967.1 156994 View on NCBI ↗
Deutzia pilosa NC_060559.1 156983 View on NCBI ↗
Deutzia scabra NC_082969.1 156860 View on NCBI ↗