Markers + reference

Gymnosphaera

4 species · Cyatheaceae · Cyatheales

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Species 4
Genome length 154–166 kb
Candidate markers 257
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 257 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
matK-rps16 Genome 1137 0.0166 1.00 45.8 yes View details
psbD-trnT-GGU Genome 1597 0.0222 1.00 61.5 yes View details
ycf3-trnS-GGA Genome 480 0.0219 1.00 51.4 yes View details
petG-trnW-CCA Genome 320 0.0401 1.00 72.8 yes View details
trnP-UGG-psaJ Genome 258 0.0304 1.00 67.1 yes View details
rrn16-rps12 Genome 1968 0.0440 1.00 79.3 yes View details
rpl32-trnP-GGG Genome 622 0.0255 0.99 61.6 yes View details
trnP-GGG-trnL-UAG Genome 182 0.0266 1.00 55.4 yes View details
psaC-ndhE Genome 376 0.0372 1.00 75.6 yes View details
rps12-rrn16 Genome 1968 0.0440 1.00 79.3 yes View details
trnR-ACG-matK Genome 4353 0.0146 0.85 55.1 no View details
rpl2-rpl23 Genome 62 0.0376 0.97 68.1 yes View details
cemA-petA Genome 229 0.0378 1.00 66.4 yes View details
petA-psbJ Genome 732 0.0143 0.99 65.5 yes View details
psaM-ycf12 Genome 244 0.0287 1.00 61.3 yes View details
rps15-ycf1 Genome 347 0.0212 0.99 61.3 yes View details
rps7-psbA Genome 871 0.0034 1.00 61.2 yes View details
psbA-rps7 Genome 871 0.0034 1.00 61.2 yes View details
trnC-GCA-trnG-GCC Genome 1296 0.0112 0.99 60.3 yes View details
trnL-UAG-ccsA Genome 239 0.0286 1.00 59.8 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
matK-rps16_p1 matK-rps16 GAATCTGCAGTCCAGCTACC GGGCAAAGGTACCTGAACAA 1459–1467 1.000 81.7
matK-rps16_p2 matK-rps16 GAATCTGCAGTCCAGCTACC TTCTGTTGCTGCCAATTCCT 2018–2036 1.000 81.5
matK-rps16_p3 matK-rps16 GAATCTGCAGTCCAGCTACC GCGAGAGGGAAAAGCCATTA 1596–1604 1.000 81.4
matK-rps16_p4 matK-rps16 GAATCTGCAGTCCAGCTACC TTCATGATCCGCGGAAAGAG 1564–1572 1.000 81.3
matK-rps16_p5 matK-rps16 GAATCTGCAGTCCAGCTACC TGGGGTTAGGCTCAAACCTA 1983–2001 1.000 81.2
psaM-ycf12_p1 psaM-ycf12 GCAATAGCCAATCTCGCAAC ACTATTAGCGCCAGAACAGC 365–413 1.000 83.7
psaM-ycf12_p2 psaM-ycf12 GCAATAGCCAATCTCGCAAC CTATTAGCGCCAGAACAGCA 364–412 1.000 83.7
psaM-ycf12_p3 psaM-ycf12 GCAATAGCCAATCTCGCAAC GTGGTCCCGATGCAACTATT 379–427 1.000 83.6
psaM-ycf12_p4 psaM-ycf12 GCAATAGCCAATCTCGCAAC TAGTGGTCCCGATGCAACTA 381–429 1.000 82.8
psaM-ycf12_p5 psaM-ycf12 GCAATAGCCAATCTCGCAAC TACTAGTGGTCCCGATGCAA 384–432 1.000 82.7
trnC-GCA-trnG-GCC_p1 trnC-GCA-trnG-GCC ATGTTGTATCAGGCGACACC GTTCGATTCCCGCTATCCG 1381–1399 1.000 73.8
trnC-GCA-trnG-GCC_p2 trnC-GCA-trnG-GCC GGATTTGCAATCCTCCGTCT GTTCGATTCCCGCTATCCG 1339–1357 1.000 73.8
trnC-GCA-trnG-GCC_p3 trnC-GCA-trnG-GCC CAGATTCGAACTGGGGGATG GTTCGATTCCCGCTATCCG 1361–1379 1.000 73.7
trnC-GCA-trnG-GCC_p4 trnC-GCA-trnG-GCC AGGATTTGCAATCCTCCGTC GTTCGATTCCCGCTATCCG 1340–1358 1.000 73.7
trnC-GCA-trnG-GCC_p5 trnC-GCA-trnG-GCC ATGTTGTATCAGGCGACACC GGTTCGATTCCCGCTATCC 1382–1400 1.000 73.6
psbD-trnT-GGU_p1 psbD-trnT-GGU TTTTCCAATGGCGATGGTCA TGGTAGGCCCCTTTAACTCA 1696–1701 1.000 82.1
psbD-trnT-GGU_p2 psbD-trnT-GGU TTTCCAATGGCGATGGTCAT TGGTAGGCCCCTTTAACTCA 1695–1700 1.000 81.6
psbD-trnT-GGU_p3 psbD-trnT-GGU CGGACCAACCTACGAAAACA TGGTAGGCCCCTTTAACTCA 1778–1783 1.000 81.5
psbD-trnT-GGU_p4 psbD-trnT-GGU ATCTTTCGGCTCCTTGGAAG TGGTAGGCCCCTTTAACTCA 1717–1722 1.000 79.4
psbD-trnT-GGU_p5 psbD-trnT-GGU CTTTCGGCTCCTTGGAAGAT TGGTAGGCCCCTTTAACTCA 1715–1720 1.000 79.4
ycf3-trnS-GGA_p1 ycf3-trnS-GGA GTCATTTCTCTGAGATCTAGGCA TGCTACACCTTAAACCGCTC 533–536 1.000 54.5
ycf3-trnS-GGA_p2 ycf3-trnS-GGA TGTCATTTCTCTGAGATCTAGGC TGCTACACCTTAAACCGCTC 534–537 1.000 54.5
ycf3-trnS-GGA_p3 ycf3-trnS-GGA GTCATTTCTCTGAGATCTAGGCA GTGCTACACCTTAAACCGCT 534–537 1.000 53.6
ycf3-trnS-GGA_p4 ycf3-trnS-GGA TGTCATTTCTCTGAGATCTAGGC GTGCTACACCTTAAACCGCT 535–538 1.000 53.6
ycf3-trnS-GGA_p5 ycf3-trnS-GGA GTGGTCGGTAGAATTTGTAACA TGCTACACCTTAAACCGCTC 595–598 1.000 53.5
cemA-petA_p1 cemA-petA CGCTTCGTTTCAACCTTTCC ATGGGCAGTTTGCTTTACCA 437–452 1.000 82.4
cemA-petA_p2 cemA-petA GCTTCGTTTCAACCTTTCCG ATGGGCAGTTTGCTTTACCA 436–451 1.000 82.4
cemA-petA_p3 cemA-petA TCTCGCTTCGTTTCAACCTT ATGGGCAGTTTGCTTTACCA 440–455 1.000 80.8
cemA-petA_p4 cemA-petA CGCTTCGTTTCAACCTTTCC TGGGCAGTTTGCTTTACCAA 436–451 1.000 80.7
cemA-petA_p5 cemA-petA GCTTCGTTTCAACCTTTCCG TGGGCAGTTTGCTTTACCAA 435–450 1.000 80.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Gymnosphaera andersonii PV567661.1 155232 View on NCBI ↗
Gymnosphaera denticulata NC_058591.1 154046 View on NCBI ↗
Gymnosphaera khasyana OR575071.1 155226 View on NCBI ↗
Gymnosphaera podophylla NC_038150.1 166151 View on NCBI ↗