Markers + reference

Nephrolepis

2 species · Nephrolepidaceae · Polypodiales

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Species 2
Genome length 149–150 kb
Candidate markers 274
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 8 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhB LSC 1198 0.0939 0.99 79.7 yes View details
matK LSC 1494 0.0877 1.00 77.9 yes View details
matK-ycf94 LSC 443 0.1009 0.98 77.3 yes View details
trnS-GCU-ycf12 LSC 583 0.1080 0.98 83.9 yes View details
psbM-petN LSC 1148 0.0971 0.98 84.1 yes View details
trnC-GCA-trnG-GCC LSC 441 0.1305 0.92 85.2 yes View details
petA-psbJ LSC 734 0.1042 0.94 83.5 yes View details
ndhF SSC 2244 0.0659 0.99 73.6 yes View details
rpl32-trnP-GGG SSC 594 0.1127 0.96 83.1 yes View details
trnP-GGG-trnL-UAG SSC 299 0.1544 0.87 78.7 yes View details
trnL-UAG-ccsA SSC 282 0.1348 1.00 72.9 yes View details
trnT-GGU-trnfM-CAU LSC 464 0.0945 0.98 83.8 yes View details
rpoB-trnD-GUC LSC 628 0.0805 0.99 83.5 yes View details
petG-trnW-CCA LSC 268 0.1158 0.97 80.9 yes View details
psbD-trnT-GGU LSC 1345 0.0739 0.98 79.7 yes View details
ndhC-trnV-UAC LSC 480 0.0861 0.99 78.7 yes View details
atpH-atpI LSC 706 0.0799 0.97 78.5 yes View details
trnL-UAA-trnF-GAA LSC 321 0.1190 0.97 78.4 yes View details
psaC-ndhE SSC 288 0.1176 0.94 78.2 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
ndhB_p1 ndhB GCTTATGAAGGATCAAGCCCA TTGATGGGTGGAGCAAGTTC 607–642 1.000 79.2
ndhB_p2 ndhB GCTTATGAAGGATCAAGCCCA TTGGTCACCCTTTATGTGGC 715–750 1.000 78.4
ndhB_p3 ndhB GCTTATGAAGGATCAAGCCCA GGTTTAGCCGGAATGGTTCT 751–786 1.000 77.9
ndhB_p4 ndhB GCTTATGAAGGATCAAGCCCA CTATATGGAACGTCTGGCGG 559 0.500 51.0
ndhB_p5 ndhB GCTTATGAAGGATCAAGCCCA GGGGACACAAAAACTTCCCT 301 0.500 50.8
matK_p1 matK AGAACCATTCCGGCTAAACC TCAACAGCAACAGTTCGTGA 2826–2853 1.000 87.4
matK_p2 matK GACCAAATCATTTGCTCGGC TCAACAGCAACAGTTCGTGA 2875 0.500 59.2
matK_p3 matK GACCAAATCATTTGCTCGGC TCGGAGGGACTACTGGTTTT 2672 0.500 59.1
matK_p4 matK GACCAAATCATTTGCTCGGC TTCGGAGGGACTACTGGTTT 2673 0.500 59.1
matK_p5 matK GACCAAATCATTTGCTCGGC TTTCGGAGGGACTACTGGTT 2674 0.500 59.1
matK-ycf94_p1 matK-ycf94 CTTGGTAACGGACGCTATCA TCGGAGGGACTACTGGTTTT 778–779 1.000 83.5
matK-ycf94_p2 matK-ycf94 CTTGGTAACGGACGCTATCA TTCGGAGGGACTACTGGTTT 779–780 1.000 83.5
matK-ycf94_p3 matK-ycf94 CTTGGTAACGGACGCTATCA TTTCGGAGGGACTACTGGTT 780–781 1.000 83.5
matK-ycf94_p4 matK-ycf94 CTTGGTAACGGACGCTATCA TCAACAGCAACAGTTCGTGA 981–982 1.000 83.0
matK-ycf94_p5 matK-ycf94 CTTGGTAACGGACGCTATCA AGCCGCATGAATCTAACGTT 1207 0.500 55.2
trnS-GCU-ycf12_p1 trnS-GCU-ycf12 GCAATCCGACGCTTTAAACC TGATGCAACTACCAAAGCCA 665–673 1.000 85.3
trnS-GCU-ycf12_p2 trnS-GCU-ycf12 CAATCCGACGCTTTAAACCG TGATGCAACTACCAAAGCCA 664–672 1.000 85.0
trnS-GCU-ycf12_p3 trnS-GCU-ycf12 GCAATCCGACGCTTTAAACC TGCAACTACCAAAGCCAAGA 662–670 1.000 84.8
trnS-GCU-ycf12_p4 trnS-GCU-ycf12 CAATCCGACGCTTTAAACCG TGCAACTACCAAAGCCAAGA 661–669 1.000 84.5
trnS-GCU-ycf12_p5 trnS-GCU-ycf12 GCAATCCGACGCTTTAAACC GGTCCTGATGCAACTACCAA 670–678 1.000 83.6
atpH-atpI_p1 atpH-atpI TTCTGGCTGTCTCGCAATAC CCACGGAAGGCCATCATTAA 858–884 1.000 86.4
atpH-atpI_p2 atpH-atpI TTCTGGCTGTCTCGCAATAC GTTGGTAGTAGCTGTTCCCG 989–1015 1.000 86.2
atpH-atpI_p3 atpH-atpI GCTAGGGCTACAACCAATCC GTTGGTAGTAGCTGTTCCCG 1075–1101 1.000 85.8
atpH-atpI_p4 atpH-atpI AAACAATATCTGGTCCGGCC GTTGGTAGTAGCTGTTCCCG 1437 0.500 59.5
atpH-atpI_p5 atpH-atpI AGTGGGGACTCGATTGGTTA GTTGGTAGTAGCTGTTCCCG 1240 0.500 59.5
rpoB-trnD-GUC_p1 rpoB-trnD-GUC TGCAAGTTCTGGCACTACG GAGTTCATCGGGATTGACGG 734–741 1.000 74.1
rpoB-trnD-GUC_p2 rpoB-trnD-GUC TGCAAGTTCTGGCACTACG GGAGTTCATCGGGATTGACG 735–742 1.000 74.1
rpoB-trnD-GUC_p3 rpoB-trnD-GUC GAATTTGTGCAAGTTCTGGCA GAGTTCATCGGGATTGACGG 741–748 1.000 73.9
rpoB-trnD-GUC_p4 rpoB-trnD-GUC GAATTTGTGCAAGTTCTGGCA GGAGTTCATCGGGATTGACG 742–749 1.000 73.9
rpoB-trnD-GUC_p5 rpoB-trnD-GUC TGAATTTGTGCAAGTTCTGGC GAGTTCATCGGGATTGACGG 742–749 1.000 73.9

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
Nephrolepis biserrata NC_044683.1 149643 View on NCBI ↗
Nephrolepis cordifolia MN623365.1 149152 View on NCBI ↗