Markers + reference

Distylium

12 species · Hamamelidaceae · Saxifragales

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Species 12
Genome length 159–159 kb
Candidate markers 266
Primer pairs 110

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 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1670 0.0013 1.00 47.0 yes View details
psbK-psbI LSC 338 0.0035 1.00 41.8 yes View details
trnS-GCU-trnG-GCC LSC 840 0.0017 1.00 43.9 yes View details
rpoC2 LSC 4164 0.0005 1.00 44.9 yes View details
rpoC1 LSC 2788 0.0008 1.00 47.9 yes View details
trnT-UGU-trnL-UAA LSC 1032 0.0018 1.00 52.7 yes View details
rbcL-accD LSC 618 0.0020 1.00 54.0 yes View details
accD LSC 1530 0.0008 1.00 31.3 yes View details
rpl20-rps12 LSC 808 0.0009 1.00 54.2 yes View details
ndhA SSC 2174 0.0014 1.00 56.7 yes View details
rps15-ycf1 SSC 377 0.0034 1.00 51.2 yes View details
ycf1 SSC 5577 0.0013 1.00 50.4 yes View details
trnC-GCA-petN LSC 840 0.0011 1.00 59.0 yes View details
rpoB-trnC-GCA LSC 1154 0.0010 1.00 57.4 yes View details
rpl32-trnL-UAG SSC 1059 0.0017 1.00 56.5 yes View details
petN-psbM LSC 1181 0.0008 1.00 52.8 yes View details
atpF LSC 1293 0.0008 1.00 52.0 yes View details
ndhF SSC 2238 0.0009 1.00 51.9 yes View details
atpH-atpI LSC 1134 0.0006 1.00 51.5 yes View details
trnT-GGU-psbD LSC 1361 0.0005 1.00 51.5 yes View details
ndhF-rpl32 SSC 1062 0.0015 1.00 51.4 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 110 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 1742–1752 1.000 80.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 1744–1754 1.000 79.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1735–1745 1.000 79.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CATGTCTTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 1745–1755 1.000 78.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGTCTTTCAAGTCGCACGTT GAGGTTCGAATCCTTCCGTC 1743–1753 1.000 77.6
psbK-psbI_p1 psbK-psbI CCAAATTACCCGAGGCCTAC GGAATCCGAAGATGAAGAGAGA 569–570 1.000 57.3
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGAATCCGAAGATGAAGAGAGA 483–484 1.000 57.3
psbK-psbI_p3 psbK-psbI CCAAATTACCCGAGGCCTAC AGGAATCCGAAGATGAAGAGAG 570–571 1.000 57.2
psbK-psbI_p4 psbK-psbI GTTTGGCAAGCTGCTGTAAG AGGAATCCGAAGATGAAGAGAG 484–485 1.000 57.2
psbK-psbI_p5 psbK-psbI CCAAATTACCCGAGGCCTAC AGGAATCCGAAGATGAAGAGA 570–571 1.000 55.7
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAATTAAACCGAGGGACCCC 952–965 1.000 80.2
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAATTAAACCGAGGGACCCC 951–964 1.000 80.2
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA GAATTAAACCGAGGGACCCC 1006–1019 1.000 79.0
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC TGGAAACGGAAAGAGAGGGA GAATTAAACCGAGGGACCCC 1011–1024 1.000 78.0
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AGCAATCCGACGCTTTAGTC GAATTAAACCGAGGGACCCC 954–967 1.000 77.4
atpF_p1 atpF GGCTCGAATGGTTACCATGA GAGGGGCGAAGTGATACAAA 1437–1443 1.000 74.9
atpF_p2 atpF GGCTCGAATGGTTACCATGA AAAGGAGGGGCGAAGTGATA 1441–1447 1.000 74.7
atpF_p3 atpF GGCTCGAATGGTTACCATGA TAAAACAAAGGAGGGGCGAA 1447–1453 1.000 72.8
atpF_p4 atpF GGCTCGAATGGTTACCATGA AAAACAAAGGAGGGGCGAAG 1446–1452 1.000 72.7
atpF_p5 atpF ACTAATTTCGTCGGCTCGAA GAGGGGCGAAGTGATACAAA 1449–1455 1.000 72.4
atpH-atpI_p1 atpH-atpI AACAGAAGCGGCAGAAATCA CGAATCCATGGAGGGTCATC 1180–1193 1.000 79.0
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT CGAATCCATGGAGGGTCATC 1238–1251 1.000 78.9
atpH-atpI_p3 atpH-atpI CAGCAGCAATAACAGAAGCG CGAATCCATGGAGGGTCATC 1190–1203 1.000 78.4
atpH-atpI_p4 atpH-atpI GCAGTACCTTGACCAACTCC CGAATCCATGGAGGGTCATC 1242–1255 1.000 78.2
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC CGAATCCATGGAGGGTCATC 1197–1210 1.000 78.1
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 (12)

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

Species Accession Length (bp) Link
Distylium buxifolium NC_059888.1 159084 View on NCBI ↗
Distylium chinense NC_059885.1 159087 View on NCBI ↗
Distylium cuspidatum NC_059890.1 159068 View on NCBI ↗
Distylium dunnianum NC_059882.1 159097 View on NCBI ↗
Distylium elaeagnoides NC_059892.1 159094 View on NCBI ↗
Distylium gracile NC_059889.1 159127 View on NCBI ↗
Distylium lepidotum NC_059891.1 159041 View on NCBI ↗
Distylium macrophyllum NC_059884.1 159095 View on NCBI ↗
Distylium myricoides NC_059883.1 159093 View on NCBI ↗
Distylium pingpienense NC_059887.1 159081 View on NCBI ↗
Distylium racemosum NC_059886.1 159107 View on NCBI ↗
Distylium tsiangii MN711651.1 159125 View on NCBI ↗