Markers + reference

Ostrya

3 species · Betulaceae · Fagales

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Species 3
Genome length 159–159 kb
Candidate markers 246
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 246 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCT-trnR-TCT LSC 1826 0.0022 1.00 60.5 yes View details
petN-psbM LSC 931 0.0043 1.00 45.3 yes View details
trnE-TTC-trnT-GGT LSC 823 0.0097 1.00 42.6 yes View details
psbC LSC 1464 0.0219 1.00 45.9 yes View details
trnN-GTT-ndhF SSC 1673 0.0028 1.00 47.8 yes View details
ycf1 SSC 5751 0.0017 1.00 47.3 yes View details
trnY-GTA-trnE-TTC LSC 60 0.0889 1.00 63.0 yes View details
atpH-atpI LSC 1214 0.0025 1.00 61.3 yes View details
ndhC-trnM-CAT LSC 1421 0.0028 1.00 60.6 yes View details
psaA-ycf3 LSC 773 0.0026 1.00 60.4 yes View details
trnH-GTG-psbA LSC 409 0.0081 1.00 60.0 yes View details
rps16 LSC 1132 0.0035 1.00 60.0 yes View details
trnT-TGT-trnF-GAA LSC 1791 0.0019 1.00 59.7 yes View details
clpP LSC 2029 0.0013 0.99 58.3 yes View details
ndhA SSC 2297 0.0015 1.00 58.1 yes View details
psaJ-rpl33 LSC 479 0.0028 1.00 58.0 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GTG-psbA_p1 trnH-GTG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 525–531 1.000 79.5
trnH-GTG-psbA_p2 trnH-GTG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 539–545 1.000 79.4
trnH-GTG-psbA_p3 trnH-GTG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 538–544 1.000 79.4
trnH-GTG-psbA_p4 trnH-GTG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 540–546 1.000 79.4
trnH-GTG-psbA_p5 trnH-GTG-psbA TATTTATGGGCGAACGACGG GCGCTAACCTTGGTATGGAA 586–592 1.000 79.3
rps16_p1 rps16 GGGGGTTGTATAGAAAGGGT TGTATCGACCGAACCAATGA 1308–1332 1.000 56.6
rps16_p2 rps16 GGGGGTTGTATAGAAAGGGTT TGTATCGACCGAACCAATGA 1308–1332 1.000 54.9
rps16_p3 rps16 GGGGGTTGTATAGAAAGGGT ATGTATCGACCGAACCAATGA 1309–1333 1.000 52.8
rps16_p4 rps16 GGGGGTTGTATAGAAAGGGT TGTATCGACCGAACCAATGAT 1308–1332 1.000 52.8
rps16_p5 rps16 GGGGGTTGTATAGAAAGGGTT TGTATCGACCGAACCAATGAT 1308–1332 1.000 51.0
trnS-GCT-trnR-TCT_p1 trnS-GCT-trnR-TCT CAATCCGACGCTTTAGTCCA AGAAGACCTCTGTCCTATCCA 1897–1913 1.000 65.5
trnS-GCT-trnR-TCT_p2 trnS-GCT-trnR-TCT AATCCGACGCTTTAGTCCAC AGAAGACCTCTGTCCTATCCA 1896–1912 1.000 65.5
trnS-GCT-trnR-TCT_p3 trnS-GCT-trnR-TCT CAATCCGACGCTTTAGTCCA AGGTTTAGAAGACCTCTGTCCT 1903–1919 1.000 64.9
trnS-GCT-trnR-TCT_p4 trnS-GCT-trnR-TCT AATCCGACGCTTTAGTCCAC AGGTTTAGAAGACCTCTGTCCT 1902–1918 1.000 64.8
trnS-GCT-trnR-TCT_p5 trnS-GCT-trnR-TCT ACAAAAGCGGAAAGAGAGGG AGAAGACCTCTGTCCTATCCA 1957–1973 1.000 64.7
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1259–1301 1.000 81.5
atpH-atpI_p2 atpH-atpI GATCCCTTCTACAGCTTGGC TTTTGCAACTTTAGCTGCGG 1344–1386 1.000 81.3
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCTGCGG 1260–1302 1.000 80.3
atpH-atpI_p4 atpH-atpI CGATCCCTTCTACAGCTTGG TTTTGCAACTTTAGCTGCGG 1345–1387 1.000 79.8
atpH-atpI_p5 atpH-atpI ATAGAAGCAAGACCGACAGC TTTTGCAACTTTAGCTGCGG 1292–1334 1.000 79.3
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 1093 1.000 68.0
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTC 1093 1.000 63.8
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTCT 1094 1.000 62.0
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTCT 1085 1.000 62.0
petN-psbM_p5 petN-psbM ATGGGGTAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 1032 1.000 61.6
trnY-GTA-trnE-TTC_p1 trnY-GTA-trnE-TTC TCTGGGGAACAACAAATGGG CATAGTATGATGGCGGTCGG 298 0.667 66.6
trnY-GTA-trnE-TTC_p2 trnY-GTA-trnE-TTC GGATTTGGATCTGTCGGGAC CATAGTATGATGGCGGTCGG 820–821 0.667 66.6
trnY-GTA-trnE-TTC_p3 trnY-GTA-trnE-TTC GCAAATGAACGGCGGTAAAA CATAGTATGATGGCGGTCGG 369 0.667 66.6
trnY-GTA-trnE-TTC_p4 trnY-GTA-trnE-TTC TTCCGATCAGGCATTTCTGG CATAGTATGATGGCGGTCGG 313 0.667 66.3
trnY-GTA-trnE-TTC_p5 trnY-GTA-trnE-TTC TCTGGGGAACAACAAATGGG ATACTTGCCCCCATCGTCTA 276 0.667 65.8

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
Ostrya chinensis NC_039817.1 159293 View on NCBI ↗
Ostrya japonica NC_039816.1 159231 View on NCBI ↗
Ostrya rehderiana NC_028349.1 159347 View on NCBI ↗