Markers + reference

Sycopsis

2 species · Hamamelidaceae · Saxifragales

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Species 2
Genome length 159–159 kb
Candidate markers 273
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG LSC 840 0.0048 0.99 55.4 yes View details
atpF-atpH LSC 450 0.0111 1.00 62.0 yes View details
rps2-rpoC2 LSC 241 0.0290 1.00 69.2 yes View details
rpoC2 LSC 4164 0.0017 1.00 48.8 yes View details
rpoC1 LSC 2788 0.0022 1.00 57.3 yes View details
rpoB-trnC-GCA LSC 1146 0.0070 1.00 62.9 yes View details
accD-psaI LSC 694 0.0144 1.00 52.9 yes View details
psaJ-rpl33 LSC 429 0.0047 1.00 44.0 yes View details
rpl32-trnL-UAG SSC 1059 0.0057 0.99 50.4 yes View details
ndhA SSC 2174 0.0051 1.00 60.3 yes View details
ndhD-psaC SSC 110 0.0182 1.00 63.0 yes View details
ndhK-ndhC LSC 59 0.0169 1.00 62.2 yes View details
petD-rpoA LSC 188 0.0110 0.97 61.9 yes View details
trnK-UUU-rps16 LSC 853 0.0047 1.00 61.4 yes View details
atpB-rbcL LSC 741 0.0040 1.00 61.1 yes View details
petN-psbM LSC 1182 0.0025 1.00 60.4 yes View details
petB LSC 1432 0.0028 1.00 60.4 yes View details
trnH-GUG LSC 74 0.0135 1.00 60.3 no View details
matK LSC 1515 0.0026 1.00 60.2 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK_p1 matK ACTGCATGAACATTTCAGAATCG AGTTTACCTGTCTCCGAGGT 1722 1.000 53.6
matK_p2 matK CTGCATGAACATTTCAGAATCGA AGTTTACCTGTCTCCGAGGT 1721 1.000 51.9
matK_p3 matK TCAACCTTTACTGCATGAACA AGTTTACCTGTCTCCGAGGT 1731 1.000 51.5
matK_p4 matK TGCATGAACATTTCAGAATCGA AGTTTACCTGTCTCCGAGGT 1720 1.000 51.4
matK_p5 matK CAGTTGATTCAACCTTTACTGCA AGTTTACCTGTCTCCGAGGT 1739 1.000 50.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGAAGGCGGAGGTTTTTACG 940–943 1.000 77.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGAAGGCGGAGGTTTTTACG 939–942 1.000 77.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC AGAAGGCGGAGGTTTTTACG 955–958 1.000 76.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AGAAGGCGGAGGTTTTTACG 949–952 1.000 76.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTTTTTACGGAACTTCGCC 929–932 1.000 76.4
trnS-GCU-trnG_p1 trnS-GCU-trnG CAATCCGACGCTTTAGTCCA GAATTAAACCGAGGGACCCC 953–956 1.000 80.7
trnS-GCU-trnG_p2 trnS-GCU-trnG AATCCGACGCTTTAGTCCAC GAATTAAACCGAGGGACCCC 952–955 1.000 80.7
trnS-GCU-trnG_p3 trnS-GCU-trnG ACGGAAAGAGAGGGATTCGA GAATTAAACCGAGGGACCCC 1007–1010 1.000 79.5
trnS-GCU-trnG_p4 trnS-GCU-trnG TGGAAACGGAAAGAGAGGGA GAATTAAACCGAGGGACCCC 1012–1015 1.000 78.5
trnS-GCU-trnG_p5 trnS-GCU-trnG AGCAATCCGACGCTTTAGTC GAATTAAACCGAGGGACCCC 955–958 1.000 77.9
atpF-atpH_p1 atpF-atpH CAGTGACCCAAGGAAACGAA CGGAGGGAAAAATACGAGGT 604–617 1.000 74.9
atpF-atpH_p2 atpF-atpH CAGTGACCCAAGGAAACGAA CGAGGCGGAGGGAAAAATAC 609–622 1.000 74.7
atpF-atpH_p3 atpF-atpH CAGTGACCCAAGGAAACGAA GAGGCGGAGGGAAAAATACG 608–621 1.000 74.7
atpF-atpH_p4 atpF-atpH CAGTGACCCAAGGAAACGAA GCGGAGGGAAAAATACGAGG 605–618 1.000 74.7
atpF-atpH_p5 atpF-atpH CAGTGACCCAAGGAAACGAA GGCGGAGGGAAAAATACGAG 606–619 1.000 74.7
rps2-rpoC2_p1 rps2-rpoC2 ACCAAAATGAACCCCTGCTT TTCGAGGGGAAAATGAGAGA 421 1.000 63.4
rps2-rpoC2_p2 rps2-rpoC2 AATGAACCCCTGCTTCCATC TTCGAGGGGAAAATGAGAGA 416 1.000 63.0
rps2-rpoC2_p3 rps2-rpoC2 GAACCCCTGCTTCCATCATC TTCGAGGGGAAAATGAGAGA 413 1.000 61.7
rps2-rpoC2_p4 rps2-rpoC2 ACCAAAATGAACCCCTGCTT TCGAGGGGAAAATGAGAGAT 420 1.000 61.5
rps2-rpoC2_p5 rps2-rpoC2 GACCAAAATGAACCCCTGCT TTCGAGGGGAAAATGAGAGA 422 1.000 61.3
rpoC2_p1 rpoC2 AAAGCAGGATGTCCATGACG CCTGGTCGAATTGGGAGAAG 207 1.000 78.5
rpoC2_p2 rpoC2 AAAGCAGGATGTCCATGACG GTCGAATTGGGAGAAGCTGT 203 1.000 77.9
rpoC2_p3 rpoC2 GGATGTCCATGACGTGTACG CCTGGTCGAATTGGGAGAAG 201 1.000 77.0
rpoC2_p4 rpoC2 AAAGCAGGATGTCCATGACG TGGTCGGAGTCCTACTCATG 231 1.000 76.7
rpoC2_p5 rpoC2 GGATGTCCATGACGTGTACG GTCGAATTGGGAGAAGCTGT 197 1.000 76.5

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
Sycopsis sinensis NC_071198.1 159084 View on NCBI ↗
Sycopsis triplinervia PP625971.1 159375 View on NCBI ↗