Markers + reference

Pteris

7 species · Pteridaceae · Polypodiales

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Species 7
Genome length 149–164 kb
Candidate markers 270
Primer pairs 60

Genome-wide nucleotide diversity

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

Candidate markers

2 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rrn16-rps12 IRb 7391 0.2675 0.53 66.7 yes View details
rps12-rrn16 IRa 7391 0.2669 0.52 66.6 yes View details
rps4-trnL-CAA LSC 734 0.1413 1.00 85.1 yes View details
atpB-rbcL LSC 645 0.1025 0.98 84.9 yes View details
atpH-atpI LSC 685 0.1253 1.00 84.6 yes View details
rpl16 LSC 1095 0.0956 1.00 84.6 yes View details
matK-rps16 LSC 671 0.1603 1.00 84.5 yes View details
rpoB-trnD-GUC LSC 779 0.1527 1.00 84.5 yes View details
rpl2 LSC 1566 0.1041 1.00 84.5 yes View details
petB LSC 1469 0.0841 1.00 84.4 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 60 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-rps16_p1 matK-rps16 GTTTCAGCCCCTCTCTGATG AACTCGACGAAGGGTAAAGC 1402–1434 0.571 72.0
matK-rps16_p2 matK-rps16 ATGTCTGGTCCGTTTGATCG AACTCGACGAAGGGTAAAGC 1233–1236 0.571 71.3
matK-rps16_p3 matK-rps16 ATGTCTGGTCCGTTTGATCG AAGGGTAAAGCATCCGTGTC 1224–1227 0.571 71.1
matK-rps16_p4 matK-rps16 ATGTCTGGTCCGTTTGATCG GAAGGGTAAAGCATCCGTGT 1225–1228 0.571 71.1
matK-rps16_p5 matK-rps16 TGGTCCGTTTGATCGTTGTT AACTCGACGAAGGGTAAAGC 1228–1231 0.571 71.1
trnG-UCC_p1 trnG-UCC GTCTCAGCGAGCAATGTACA AAGGAGGCAACGGAACTTTT 1231–1282 0.857 85.7
trnG-UCC_p2 trnG-UCC GTCTCAGCGAGCAATGTACA AGAAGACCTCTGCCCTATCC 1075–1120 0.857 85.5
trnG-UCC_p3 trnG-UCC ATGCTAGTTCAGAATGGCGG TGGGGGCTACTTTGCAAAAT 1612–1662 0.571 72.4
trnG-UCC_p4 trnG-UCC GTCTCAGCGAGCAATGTACA TGGGGGCTACTTTGCAAAAT 1131–1176 0.571 72.3
trnG-UCC_p5 trnG-UCC CGGGAGACGTGACTCAAATT TGGGGGCTACTTTGCAAAAT 1595–1645 0.571 72.2
atpH-atpI_p1 atpH-atpI TTCCGTGAAAGCCAAACTCA CTTTACCCGCTGTGACTACC 1455–1468 0.857 81.3
atpH-atpI_p2 atpH-atpI CCCCGCCAATTTGGAAATTC CTTTACCCGCTGTGACTACC 1632 0.143 45.5
atpH-atpI_p3 atpH-atpI CCCCGCCAATTTGGAAATTC AATTGGTCAGGTGCTTCGTT 1459 0.143 45.4
atpH-atpI_p4 atpH-atpI CCCCGCCAATTTGGAAATTC ATTGGTCAGGTGCTTCGTTT 1458 0.143 45.4
atpH-atpI_p5 atpH-atpI CCCCGCCAATTTGGAAATTC ATTTTGGCTGACGAGTTGGT 1204 0.143 45.4
rpoB-trnD-GUC_p1 rpoB-trnD-GUC TCTCCGACTGAAGGTTCTGT TCTACCTTCTCCACGATCCC 1318–1330 0.571 72.2
rpoB-trnD-GUC_p2 rpoB-trnD-GUC CTGGTACATATGGATCGGCG TCTACCTTCTCCACGATCCC 1371–1383 0.571 71.8
rpoB-trnD-GUC_p3 rpoB-trnD-GUC TCTCCGACTGAAGGTTCTGT GGGGGTATTCAAGCTCCAAG 1379 0.143 45.2
rpoB-trnD-GUC_p4 rpoB-trnD-GUC CTGGTACATATGGATCGGCG GGGGGTATTCAAGCTCCAAG 1432 0.143 45.2
rpoB-trnD-GUC_p5 rpoB-trnD-GUC GCATCCTCCGGTGATTCAAT GGGGGTATTCAAGCTCCAAG 1844 0.143 45.0
rps4-trnL-CAA_p1 rps4-trnL-CAA GCGTTCTGTCAATCCGTAGT ACGTCTCCATACCTAGGCTC 958–971 0.857 84.4
rps4-trnL-CAA_p2 rps4-trnL-CAA GCGTTCTGTCAATCCGTAGT CGTCTCCATACCTAGGCTCA 957–970 0.857 84.4
rps4-trnL-CAA_p3 rps4-trnL-CAA AACGCATCTCAAGCAATTGC ACGTCTCCATACCTAGGCTC 1040–1053 0.857 84.2
rps4-trnL-CAA_p4 rps4-trnL-CAA AACGCATCTCAAGCAATTGC CGTCTCCATACCTAGGCTCA 1039–1052 0.857 84.2
rps4-trnL-CAA_p5 rps4-trnL-CAA GCGTTCTGTCAATCCGTAGT TGAGGTGATGCGAGATTTGG 1037–1050 0.571 69.9
trnL-CAA_p1 trnL-CAA AGCTCTTTAGTGAGTGGGGT CCTGAATGGCTGATCCTTCC 893 0.143 45.3
trnL-CAA_p2 trnL-CAA AGCTCTTTAGTGAGTGGGGT CTGAATGGCTGATCCTTCCC 892 0.143 45.3
trnL-CAA_p3 trnL-CAA AGCTCTTTAGTGAGTGGGGT GGGAATAATTCACCGGGGAC 1467 0.143 45.3
trnL-CAA_p4 trnL-CAA AGCTCTTTAGTGAGTGGGGT ACACCCGTATCTTAGGCGTA 1449 0.143 45.0
trnL-CAA_p5 trnL-CAA AGCTCTTTAGTGAGTGGGGT GATTCGAACTGGTGACACGA 1146 0.143 45.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Pteris arisanensis NC_083994.1 160191 View on NCBI ↗
Pteris ensiformis NC_083995.1 148985 View on NCBI ↗
Pteris multifida NC_058883.1 153916 View on NCBI ↗
Pteris semipinnata NC_060734.1 162270 View on NCBI ↗
Pteris terminalis PQ178992.1 163881 View on NCBI ↗
Pteris vittata NC_040204.1 149424 View on NCBI ↗
Pteris wallichiana NC_087773.1 153915 View on NCBI ↗