Markers + reference

Distyliopsis

3 species · Hamamelidaceae · Saxifragales

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Species 3
Genome length 159–159 kb
Candidate markers 273
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 363 0.0129 1.00 35.0 yes View details
trnK-UUU-rps16 LSC 852 0.0086 1.00 53.6 yes View details
psbZ-trnG-UCC LSC 398 0.0168 1.00 54.4 yes View details
accD LSC 1530 0.0031 1.00 46.5 yes View details
petA-psbJ LSC 1056 0.0101 1.00 53.1 yes View details
rps18 LSC 306 0.0065 1.00 31.7 yes View details
rpl32-trnL-UAG SSC 1061 0.0063 1.00 51.4 yes View details
ndhA SSC 2174 0.0067 1.00 58.1 yes View details
rps15-ycf1 SSC 377 0.0106 1.00 57.9 yes View details
atpF-atpH LSC 451 0.0089 1.00 61.6 yes View details
trnT-GGU-psbD LSC 1361 0.0044 1.00 60.9 yes View details
trnE-UUC-trnT-GGU LSC 880 0.0015 1.00 60.8 yes View details
atpA-atpF LSC 65 0.0104 0.98 60.6 yes View details
petB LSC 1432 0.0019 1.00 60.6 yes View details
trnC-GCA-petN LSC 840 0.0040 1.00 60.4 yes View details
trnL-UAA-trnF-GAA LSC 374 0.0054 1.00 60.2 yes View details
ndhH SSC 1182 0.0023 1.00 58.7 yes View details
petD-rpoA LSC 190 0.0108 0.98 58.3 yes View details
rps16 LSC 1119 0.0024 1.00 57.0 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 TCAGTGCTATGCATGGTTCC 816–824 1.000 79.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCAGTGCTATGCATGGTTCC 830–838 1.000 79.5
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAGTGCTATGCATGGTTCCT 815–823 1.000 79.5
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TCAGTGCTATGCATGGTTCC 829–837 1.000 79.4
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TCAGTGCTATGCATGGTTCC 831–839 1.000 79.4
trnK-UUU_p1 trnK-UUU TGTGAATGAATGAAGTGAGTTACA TTGCGTCGTACAATCCAGTC 2661 0.667 26.7
trnK-UUU_p2 trnK-UUU TGTGAATGAATGAAGTGAGTTACA ATTGCGTCGTACAATCCAGT 2662 0.667 26.7
trnK-UUU_p3 trnK-UUU TGTGAATGAATGAAGTGAGT TTGCGTCGTACAATCCAGTC 2661 0.667 26.7
trnK-UUU_p4 trnK-UUU TGTGAATGAATGAAGTGAGTTACA GCGTCGTACAATCCAGTCTC 2659 0.667 26.7
trnK-UUU_p5 trnK-UUU TGTGAATGAATGAAGTGAGTT TTGCGTCGTACAATCCAGTC 2661 0.667 26.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGAAGGCGGAGGTTTTTACG 939–946 1.000 78.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGAAGGCGGAGGTTTTTACG 938–945 1.000 78.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AGAAGGCGGAGGTTTTTACG 948–955 1.000 77.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTTTTTACGGAACTTCGCC 929–936 1.000 77.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTTTTTACGGAACTTCGCC 928–935 1.000 77.6
rps16_p1 rps16 GTGATCCCCACACTCTTTTT ACCGGTTCCAAACTAGAGGA 1180–1181 1.000 60.9
rps16_p2 rps16 GTGATCCCCACACTCTTTTT TGTACCGACTGAACCAATGAC 1233–1234 1.000 52.8
rps16_p3 rps16 GTGATCCCCACACTCTTTTT CCGGTTCCAAACTAGAGGAA 1179–1180 1.000 52.0
rps16_p4 rps16 GTGATCCCCACACTCTTTTT TACCGGTTCCAAACTAGAGGA 1181–1182 1.000 51.7
rps16_p5 rps16 GTGATCCCCACACTCTTTTT ACCGACTGAACCAATGACTAC 1230–1231 1.000 50.6
atpA-atpF_p1 atpA-atpF CACTTGAAGTACGGTACCGG TGTTTGGGGCGATGAAAGAA 200–202 1.000 81.0
atpA-atpF_p2 atpA-atpF CCACTTGAAGTACGGTACCG TGTTTGGGGCGATGAAAGAA 201–203 1.000 81.0
atpA-atpF_p3 atpA-atpF CACTTGAAGTACGGTACCGG ATGTTTGGGGCGATGAAAGA 201–203 1.000 79.4
atpA-atpF_p4 atpA-atpF CCACTTGAAGTACGGTACCG ATGTTTGGGGCGATGAAAGA 202–204 1.000 79.4
atpA-atpF_p5 atpA-atpF CACTTGAAGTACGGTACCGG GGTATGTTTGGGGCGATGAA 204–206 1.000 79.1
atpF-atpH_p1 atpF-atpH CAGTGACCCAAGGAAACGAA CGGAGGGAAAAATACGAGGT 604–605 1.000 75.1
atpF-atpH_p2 atpF-atpH CAGTGACCCAAGGAAACGAA CGAGGCGGAGGGAAAAATAC 609–610 1.000 75.0
atpF-atpH_p3 atpF-atpH CAGTGACCCAAGGAAACGAA GAGGCGGAGGGAAAAATACG 608–609 1.000 75.0
atpF-atpH_p4 atpF-atpH CAGTGACCCAAGGAAACGAA GCGGAGGGAAAAATACGAGG 605–606 1.000 75.0
atpF-atpH_p5 atpF-atpH CAGTGACCCAAGGAAACGAA GGCGGAGGGAAAAATACGAG 606–607 1.000 75.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Distyliopsis dunnii NC_071205.1 159078 View on NCBI ↗
Distyliopsis laurifolia NC_071202.1 159328 View on NCBI ↗
Distyliopsis tutcheri ON729374.1 159183 View on NCBI ↗