Markers + reference

Sinojackia

6 species · Styracaceae · Ericales

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Species 6
Genome length 159–159 kb
Candidate markers 266
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1746 0.0009 1.00 52.7 yes View details
ndhC-trnM-CAU LSC 2015 0.0009 1.00 52.2 yes View details
rbcL-accD LSC 1147 0.0013 1.00 53.6 yes View details
rpl16-rps3 LSC 1201 0.0009 1.00 43.9 yes View details
ycf15-trnL-CAA IRb 370 0.0065 1.00 39.5 yes View details
trnN-GUU-ndhF IRb 1400 0.0017 1.00 44.5 yes View details
ndhF-trnL-UAG SSC 2025 0.0037 1.00 51.2 yes View details
ndhD SSC 1500 0.0006 1.00 34.1 yes View details
ndhB-trnL-CAA IRa 554 0.0000 1.00 34.7 yes View details
petB LSC 1404 0.0006 1.00 50.3 yes View details
ycf3-trnS-GGA LSC 845 0.0008 1.00 46.9 yes View details
petD LSC 1257 0.0003 1.00 46.6 yes View details
rpl20-rps12 LSC 798 0.0000 0.97 45.8 yes View details
trnT-UGU-trnL-UAA LSC 948 0.0007 1.00 45.2 yes View details
trnE-UUC-trnT-GGU LSC 808 0.0004 1.00 45.1 yes View details
atpA-atpF LSC 64 0.0000 1.00 43.7 yes View details
rpoB-trnC-GCA LSC 1111 0.0008 1.00 43.7 yes View details
ndhH SSC 1182 0.0007 1.00 43.7 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 1825–1827 1.000 79.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 1827–1829 1.000 78.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1818–1820 1.000 78.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CATGTCTTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 1828–1830 1.000 77.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG AAATTTAAATGGGGCGTGGC 1882–1884 1.000 77.0
trnT-CGU_p1 trnT-CGU GGCTAATTCCCCTGTTCGAC AATATAGAGGGTATATAGGAATGAA 935–941 1.000 40.3
trnT-CGU_p2 trnT-CGU ATGGCTAATTCCCCTGTTCG AATATAGAGGGTATATAGGAATGAA 937–943 1.000 40.3
trnT-CGU_p3 trnT-CGU GCTAATTCCCCTGTTCGACA AATATAGAGGGTATATAGGAATGAA 934–940 1.000 40.3
trnT-CGU_p4 trnT-CGU TGGCTAATTCCCCTGTTCGA AATATAGAGGGTATATAGGAATGAA 936–942 1.000 40.3
trnT-CGU_p5 trnT-CGU GGCTAATTCCCCTGTTCGAC AGAGGGTATATAGGAATGAATATATT 930–936 1.000 40.3
atpA-atpF_p1 atpA-atpF ACTTGAAGTACGGTACCGGT TGGTATGTTTGGAGCGATGA 204–207 1.000 69.2
atpA-atpF_p2 atpA-atpF TTGCTCAATACGTTCACGGA TGGTATGTTTGGAGCGATGA 157–160 1.000 68.9
atpA-atpF_p3 atpA-atpF TCGCCTACTTGAAGTACGGT TGGTATGTTTGGAGCGATGA 210–213 1.000 68.5
atpA-atpF_p4 atpA-atpF ACTAATTTCGTCGGCTCGAA TGGTATGTTTGGAGCGATGA 130–133 1.000 67.5
atpA-atpF_p5 atpA-atpF ACTTGAAGTACGGTACCGGT TGGTATGTTTGGAGCGATGAA 204–207 1.000 67.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCCTTCATTTCCATCCCGGA AAAAGGATTTGCAGTCCCCC 1179 1.000 74.0
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TTCCTTCATTTCCATCCCGG AAAAGGATTTGCAGTCCCCC 1180 1.000 73.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TAAAACTCTTCCGCCAAGCC AAAAGGATTTGCAGTCCCCC 1262 1.000 73.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GCCAAGCCCTGATCAATGAA AAAAGGATTTGCAGTCCCCC 1250 1.000 73.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCCTTCATTTCCATCCCGGA GCGACACCCAGATTTGAACT 1204 1.000 73.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 947–950 1.000 78.9
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 926–929 1.000 78.5
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 923–926 1.000 78.3
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 909–912 1.000 78.1
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 888–891 1.000 78.0
ycf3-trnS-GGA_p1 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA CCCTCGGTAAACAAAAGCCT 1008 1.000 66.7
ycf3-trnS-GGA_p2 ycf3-trnS-GGA TTTCTCCTGAAGTTGTCGGA CCCTCGGTAAACAAAAGCCT 1009 1.000 66.7
ycf3-trnS-GGA_p3 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA ACGGAAAGAGAGGGATTCGA 1029 1.000 66.3
ycf3-trnS-GGA_p4 ycf3-trnS-GGA TTTCTCCTGAAGTTGTCGGA ACGGAAAGAGAGGGATTCGA 1030 1.000 66.3
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA TTCCAATGCTACGCCTTGAA 979 1.000 65.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Sinojackia huangmeiensis NC_047297.1 158758 View on NCBI ↗
Sinojackia microcarpa NC_041131.1 158739 View on NCBI ↗
Sinojackia oblongicarpa NC_080872.1 158737 View on NCBI ↗
Sinojackia rehderiana NC_035711.1 158760 View on NCBI ↗
Sinojackia sarcocarpa NC_042148.1 158737 View on NCBI ↗
Sinojackia xylocarpa NC_035418.1 158725 View on NCBI ↗