Markers + reference

Alsophila

5 species · Cyatheaceae · Cyatheales

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Species 5
Genome length 156–162 kb
Candidate markers 273
Primer pairs 105

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

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhB Genome 1299 0.0326 1.00 59.3 yes View details
matK-rps16 Genome 917 0.0426 1.00 66.9 yes View details
rpoB-trnD-GUC Genome 1158 0.0489 1.00 75.6 yes View details
trnC-GCA-trnG-GCC Genome 1511 0.1670 0.83 68.4 yes View details
psbD-trnT-GGU Genome 1628 0.0384 0.99 72.3 yes View details
rps4-trnL-CAA Genome 662 0.0444 1.00 60.2 yes View details
psbE-petL Genome 996 0.0477 1.00 65.0 yes View details
petG-trnW-CCA Genome 320 0.0581 1.00 73.2 yes View details
rpl32-trnP-GGG Genome 627 0.0530 1.00 76.2 yes View details
ccsA-ndhD Genome 419 0.0621 1.00 64.6 yes View details
trnR-ACG-trnT-UGU Genome 1466 0.0300 0.87 54.1 yes View details
ycf3-trnS-GGA Genome 498 0.0461 0.99 73.8 yes View details
ndhD-psaC Genome 153 0.0510 1.00 71.6 yes View details
ndhI-ndhA Genome 160 0.0860 0.98 70.9 yes View details
rpl23-trnI-CAU Genome 225 0.0702 0.98 68.5 yes View details
ycf1-chlN Genome 368 0.0518 1.00 68.0 yes View details
trnS-GCU-psaM Genome 331 0.0338 1.00 67.8 yes View details
petA-psbJ Genome 773 0.0388 1.00 67.0 yes View details
atpH-atpI Genome 755 0.0232 0.99 66.0 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ndhB_p1 ndhB ATACATTAGGCGGGAGGGTT CGTGGGAATCGCCTGAATAA 358–362 0.600 62.6
ndhB_p2 ndhB ATACATTAGGCGGGAGGGTT GGATTTACCTCCCCGCAAAT 273 0.600 62.6
ndhB_p3 ndhB ATACATTAGGCGGGAGGGTT TATGGCCTTTCTGGTGGAGA 684–688 0.600 62.5
ndhB_p4 ndhB ATACATTAGGCGGGAGGGTT GTATGGCCTTTCTGGTGGAG 685–689 0.600 62.4
ndhB_p5 ndhB ATACATTAGGCGGGAGGGTT GGCAGGAATGGCTTTCAAAC 577–581 0.600 62.1
matK-rps16_p1 matK-rps16 GAATCTGCAGTCCAGCTACC GGGCAAAGGTACCTGAACAA 1229–1457 1.000 85.0
matK-rps16_p2 matK-rps16 GAATCTGCAGTCCAGCTACC AGAGGATACCCGATACGCAA 1705–1718 0.600 64.8
matK-rps16_p3 matK-rps16 TCCGAGACAGAAGGGGTATC AGAGGATACCCGATACGCAA 1779–1780 0.400 55.4
matK-rps16_p4 matK-rps16 TCCGAGACAGAAGGGGTATC GGGCAAAGGTACCTGAACAA 1301–1302 0.400 55.4
matK-rps16_p5 matK-rps16 CCGAGACAGAAGGGGTATCT AGAGGATACCCGATACGCAA 1778–1779 0.400 55.3
trnS-GCU-psaM_p1 trnS-GCU-psaM ATTAGCAATCCGACGCGTTA GTTGCGAGATTGGCTATTGC 399–423 1.000 82.9
trnS-GCU-psaM_p2 trnS-GCU-psaM TTAGACCTCTCGGCCATCTC GTTGCGAGATTGGCTATTGC 382–406 1.000 82.4
trnS-GCU-psaM_p3 trnS-GCU-psaM ATTAGCAATCCGACGCGTTA TTGCGAGATTGGCTATTGCA 398–422 1.000 81.8
trnS-GCU-psaM_p4 trnS-GCU-psaM ATTAGCAATCCGACGCGTTA GGCTATTGCACTGTACCGTT 388–412 1.000 81.8
trnS-GCU-psaM_p5 trnS-GCU-psaM ATTAGCAATCCGACGCGTTA TTGGCTATTGCACTGTACCG 390–414 1.000 81.8
trnG-UCC_p1 trnG-UCC AATAGTTGCATCGGGACCAC TTCTTGGTTCAGTTGCGTGA 1593–1606 1.000 84.8
trnG-UCC_p2 trnG-UCC AATAGTTGCATCGGGACCAC AGAATCAGTTAGCCAGGGGT 1739–1752 1.000 84.5
trnG-UCC_p3 trnG-UCC CATTCCCATAGGCGGAACAA AGAATCAGTTAGCCAGGGGT 1675–1688 1.000 84.5
trnG-UCC_p4 trnG-UCC ATTCCCATAGGCGGAACAAC AGAATCAGTTAGCCAGGGGT 1674–1687 1.000 84.5
trnG-UCC_p5 trnG-UCC CAACTCCCCGCTAGAGACTA AGAATCAGTTAGCCAGGGGT 1658–1671 1.000 84.5
atpH-atpI_p1 atpH-atpI GCAGCAATAACAGAAGCAGC GGGAATCTACGGAGGGTCAT 810–819 1.000 82.0
atpH-atpI_p2 atpH-atpI AGAAGCAGCAGGAATCAAGG GGGAATCTACGGAGGGTCAT 799–808 1.000 81.8
atpH-atpI_p3 atpH-atpI GCAGCAATAACAGAAGCAGC TACAGGGGAATCTACGGAGG 815–824 1.000 81.2
atpH-atpI_p4 atpH-atpI AGAAGCAGCAGGAATCAAGG TACAGGGGAATCTACGGAGG 804–813 1.000 81.0
atpH-atpI_p5 atpH-atpI CAGCAGGAATCAAGGGGTTC GGGAATCTACGGAGGGTCAT 794–803 1.000 78.6
rpoB-trnD-GUC_p1 rpoB-trnD-GUC GAATTCGTGCAAGTTCTGGC AACCTCGCGATCGTACTAGA 1562–1620 1.000 87.6
rpoB-trnD-GUC_p2 rpoB-trnD-GUC GAATTCGTGCAAGTTCTGGC ACCTCGCGATCGTACTAGAA 1561–1619 1.000 87.6
rpoB-trnD-GUC_p3 rpoB-trnD-GUC GAATTCGTGCAAGTTCTGGC AGAACCTCGCGATCGTACTA 1564–1622 1.000 87.6
rpoB-trnD-GUC_p4 rpoB-trnD-GUC GAATTCGTGCAAGTTCTGGC GATTGACGATTCGTGGGGAA 1696–1754 1.000 87.4
rpoB-trnD-GUC_p5 rpoB-trnD-GUC TTGATCCGATTCGCGATTGT GATTGACGATTCGTGGGGAA 2061–2119 1.000 85.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Alsophila costularis NC_044080.1 156675 View on NCBI ↗
Alsophila gigantea NC_044079.1 161679 View on NCBI ↗
Alsophila latebrosa MW620065.1 155724 View on NCBI ↗
Alsophila metteniana NC_063315.1 161602 View on NCBI ↗
Alsophila spinulosa NC_012818.1 156661 View on NCBI ↗