Markers + reference

Sphaeropteris

2 species · Cyatheaceae · Cyatheales

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Species 2
Genome length 157–162 kb
Candidate markers 275
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-psaM Genome 342 0.0323 1.00 72.2 yes View details
ycf66 Genome 703 0.0259 0.99 60.8 yes View details
petA-psbJ Genome 753 0.0173 1.00 68.8 yes View details
trnT-UGU-trnR-ACG Genome 1098 0.0092 0.99 65.5 yes View details
rpl32-trnP-GGG Genome 624 0.0259 0.99 73.5 yes View details
trnL-UAG-ccsA Genome 279 0.0328 0.98 64.3 yes View details
rps15-ycf1 Genome 1134 0.0194 1.00 68.0 yes View details
trnR-ACG-trnT-UGU Genome 1098 0.0092 0.99 65.5 yes View details
trnfM-CAU-rps14 Genome 142 0.0352 1.00 71.0 yes View details
ndhH-rps15 Genome 111 0.0270 1.00 68.0 yes View details
rpl20-rps12 Genome 1055 0.0105 0.99 65.4 yes View details
infA-rps8 Genome 137 0.0219 1.00 65.1 yes View details
rps4-trnL-CAA Genome 654 0.0107 1.00 64.9 yes View details
matK-rps16 Genome 981 0.0072 0.99 63.7 yes View details
ndhF-rpl21 Genome 222 0.0180 1.00 62.9 yes View details
accD-psaI Genome 565 0.0071 1.00 62.1 yes View details
ccsA-ndhD Genome 431 0.0116 1.00 62.1 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-rps16_p1 matK-rps16 TTTCCGTAACGTCCCAAACC GGGCAAAGGTACCTGAACAA 1064–1067 1.000 77.8
matK-rps16_p2 matK-rps16 ACTTTTCCGTAACGTCCCAA GGGCAAAGGTACCTGAACAA 1067–1070 1.000 76.1
matK-rps16_p3 matK-rps16 TTTCCGTAACGTCCCAAACC ATATCGAAACGGGCAAAGGT 1074–1077 1.000 74.5
matK-rps16_p4 matK-rps16 TTTCCGTAACGTCCCAAACC GGGGCTCAAACAACAGAAAC 1104–1107 1.000 73.7
matK-rps16_p5 matK-rps16 TTTCCGTAACGTCCCAAACC ATCGAAACGGGCAAAGGTAC 1072–1075 1.000 73.4
trnS-GCU-psaM_p1 trnS-GCU-psaM ATTAGCAATCCGACGCGTTA GTTGCGAGATTGGCTATTGC 415–424 1.000 79.7
trnS-GCU-psaM_p2 trnS-GCU-psaM TTAGACCTCTCGGCCATCTC GTTGCGAGATTGGCTATTGC 398–407 1.000 79.0
trnS-GCU-psaM_p3 trnS-GCU-psaM TCTTGGAGGAGAGAGAGGGA GTTGCGAGATTGGCTATTGC 469–478 1.000 78.6
trnS-GCU-psaM_p4 trnS-GCU-psaM ATTAGCAATCCGACGCGTTA TTGCGAGATTGGCTATTGCA 414–423 1.000 78.6
trnS-GCU-psaM_p5 trnS-GCU-psaM ATTAGCAATCCGACGCGTTA GGCTATTGCACTGTACCGTT 404–413 1.000 78.5
ycf66_p1 ycf66 TTCGTAGCCACTGCACTTTT CTGCAGTTTGGGGAAGAAGT 1303–1307 1.000 81.4
ycf66_p2 ycf66 AGGTTGCAACAGCTGATTGA CTGCAGTTTGGGGAAGAAGT 1608–1612 1.000 81.2
ycf66_p3 ycf66 TGAGGTTGCAACAGCTGATT CTGCAGTTTGGGGAAGAAGT 1610–1614 1.000 81.2
ycf66_p4 ycf66 AGGTTGCAACAGCTGATTGA AGACGGAGGATTGCAAATCC 2122–2124 1.000 80.8
ycf66_p5 ycf66 TGAGGTTGCAACAGCTGATT AGACGGAGGATTGCAAATCC 2124–2126 1.000 80.8
trnfM-CAU-rps14_p1 trnfM-CAU-rps14 AAGGTTATGAGCCTTGCGAG CGACCCAGATCCAATTACCG 287–308 1.000 80.0
trnfM-CAU-rps14_p2 trnfM-CAU-rps14 TTTGAACCCGTGACCTCAAG CGACCCAGATCCAATTACCG 304–325 1.000 79.9
trnfM-CAU-rps14_p3 trnfM-CAU-rps14 ACAGGATTTGAACCCGTGAC CGACCCAGATCCAATTACCG 310–331 1.000 79.3
trnfM-CAU-rps14_p4 trnfM-CAU-rps14 GATTTGAACCCGTGACCTCA CGACCCAGATCCAATTACCG 306–327 1.000 78.8
trnfM-CAU-rps14_p5 trnfM-CAU-rps14 CCTTTGCGGAGACAGGATTT CGACCCAGATCCAATTACCG 321–342 1.000 78.7
rps4-trnL-CAA_p1 rps4-trnL-CAA TCCCTGTAAGCCCTGGTAAA CTGAATCTGGGAGCTGTCAC 812–813 1.000 80.1
rps4-trnL-CAA_p2 rps4-trnL-CAA TTCCCTGTAAGCCCTGGTAA CTGAATCTGGGAGCTGTCAC 813–814 1.000 80.1
rps4-trnL-CAA_p3 rps4-trnL-CAA TTTCCCTGTAAGCCCTGGTA CTGAATCTGGGAGCTGTCAC 814–815 1.000 80.1
rps4-trnL-CAA_p4 rps4-trnL-CAA AAGCAGATTGATCAGCAGCA CTGAATCTGGGAGCTGTCAC 860–861 1.000 79.5
rps4-trnL-CAA_p5 rps4-trnL-CAA AGCAGATTGATCAGCAGCAA CTGAATCTGGGAGCTGTCAC 859–860 1.000 79.5
accD-psaI_p1 accD-psaI GAAGGGTGTTTTGAGCGAGA AGGGTAGATAGGACGCTGTC 648–656 1.000 79.4
accD-psaI_p2 accD-psaI GAAGGGTGTTTTGAGCGAGA GAGGGTAGATAGGACGCTGT 649–657 1.000 79.4
accD-psaI_p3 accD-psaI AGCCTTATTACTCAGCCCCT AGGGTAGATAGGACGCTGTC 622–630 1.000 78.8
accD-psaI_p4 accD-psaI AGCCTTATTACTCAGCCCCT GAGGGTAGATAGGACGCTGT 623–631 1.000 78.8
accD-psaI_p5 accD-psaI TGAGCGAGATATCTGAGCCT AGGGTAGATAGGACGCTGTC 637–645 1.000 78.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Sphaeropteris brunoniana NC_051561.1 156659 View on NCBI ↗
Sphaeropteris lepifera NC_063825.1 162114 View on NCBI ↗