Markers + reference

Halesia

2 species · Styracaceae · Ericales

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Species 2
Genome length 159–159 kb
Candidate markers 271
Primer pairs 115

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 11 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 862 0.0105 0.99 56.3 yes View details
rps16-trnQ-UUG LSC 1734 0.0064 1.00 56.9 yes View details
trnS-GCU-trnG-GCC LSC 698 0.0101 0.99 54.7 yes View details
trnT-GGU-psbD LSC 1487 0.0061 1.00 53.5 yes View details
trnF-GAA-ndhJ LSC 716 0.0168 1.00 57.7 yes View details
rbcL-accD LSC 683 0.0075 0.98 64.9 yes View details
ycf4-cemA LSC 956 0.0096 0.98 55.7 yes View details
psbE-petL LSC 1286 0.0101 1.00 53.8 yes View details
ycf1 IRb 1068 0.0009 1.00 59.5 no View details
ndhF-rpl32 SSC 956 0.0110 0.95 57.6 yes View details
rpl32-trnL-UAG SSC 912 0.0121 0.99 56.5 yes View details
ccsA SSC 966 0.0114 1.00 65.3 yes View details
ndhA SSC 2199 0.0078 1.00 57.1 yes View details
ycf1 SSC 5658 0.0085 1.00 42.5 yes View details
ndhE-ndhG SSC 219 0.0228 1.00 65.6 yes View details
rps15-ycf1 SSC 379 0.0185 1.00 64.8 yes View details
rps3 LSC 657 0.0076 1.00 63.1 yes View details
petA-psbJ LSC 1021 0.0069 1.00 62.9 yes View details
rpoB-trnC-GCA LSC 1111 0.0063 1.00 62.6 yes View details
atpB-rbcL LSC 770 0.0052 1.00 61.9 yes View details
trnH-GUG-psbA LSC 390 0.0128 1.00 61.7 yes View details
matK LSC 1524 0.0046 1.00 61.3 yes View details
rps12-clpP LSC 139 0.0144 1.00 60.8 yes View details
rpl2 IRb 1489 0.0013 1.00 59.5 yes View details
rpl2 IRa 1489 0.0013 1.00 59.5 no 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 115 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 516–555 1.000 77.0
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCGTGCTAACCTTGGTATGG 517–556 1.000 76.8
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT ACCGTGCTAACCTTGGTATG 517–556 1.000 76.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC ACCGTGCTAACCTTGGTATG 518–557 1.000 76.3
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 509–548 1.000 75.4
matK_p1 matK ACGCGGTCTCATAACAAATCA TGTTTTGACCGTATCGCACT 1621 1.000 70.8
matK_p2 matK ACGCGGTCTCATAACAAATCA CCTTGTTTTGACCGTATCGC 1624 1.000 67.9
matK_p3 matK CGCGGTCTCATAACAAATCA TGTTTTGACCGTATCGCACT 1620 1.000 65.1
matK_p4 matK ACGCGGTCTCATAACAAATC TGTTTTGACCGTATCGCACT 1621 1.000 65.1
matK_p5 matK ACGCGGTCTCATAACAAATCA TTGTTTTGACCGTATCGCAC 1622 1.000 64.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA AAGGGCGGAGGTTTTTAAGG 995–996 1.000 80.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC AAGGGCGGAGGTTTTTAAGG 996–997 1.000 80.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 ATGGACGAATCCCTTGCTTC AAGGGCGGAGGTTTTTAAGG 1000–1001 1.000 80.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT AAGGGCGGAGGTTTTTAAGG 998–999 1.000 80.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA GGGCGGAGGTTTTTAAGGAA 993–994 1.000 80.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 1814–1824 1.000 79.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 1816–1826 1.000 78.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1807–1817 1.000 78.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CATGTCTTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 1817–1827 1.000 78.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG AAATTTAAATGGGGCGTGGC 1871–1881 1.000 77.4
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC AGGAAACGGAAAGAGAGGGA ACGAATCGCACTTTTACCACT 820–826 1.000 71.2
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AGGAAACGGAAAGAGAGGGA ACGAATCGCACTTTTACCAC 820–826 1.000 71.1
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA ACGAATCGCACTTTTACCACT 766–772 1.000 71.1
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA ACGAATCGCACTTTTACCAC 766–772 1.000 71.1
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA ACGAATCGCACTTTTACCACT 815–821 1.000 70.2
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCCTTCATTTCCATCCCGGA AAAAGGATTTGCAGTCCCCC 1177–1179 1.000 74.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TTCCTTCATTTCCATCCCGG AAAAGGATTTGCAGTCCCCC 1178–1180 1.000 74.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GCCAAGCCCTGATCAATGAA AAAAGGATTTGCAGTCCCCC 1248–1250 1.000 73.6
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCCTTCATTTCCATCCCGGA GCGACACCCAGATTTGAACT 1202–1204 1.000 73.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TTCCTTCATTTCCATCCCGG GCGACACCCAGATTTGAACT 1203–1205 1.000 73.3

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
Halesia carolina NC_041127.1 159018 View on NCBI ↗
Halesia diptera NC_041128.1 158849 View on NCBI ↗