Markers + reference

Lygodium

8 species · Lygodiaceae · Schizaeales

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Species 8
Genome length 157–164 kb
Candidate markers 268
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 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
matK-rps16 LSC 1219 0.0749 0.96 83.3 yes View details
atpH-atpI LSC 679 0.0742 0.98 83.9 yes View details
rpoB-trnC-GCA LSC 872 0.0848 0.97 83.8 yes View details
trnE-UUC-trnG-GCC LSC 700 0.0721 0.95 84.9 yes View details
rpl14-rpl16 LSC 471 0.1000 0.96 80.7 yes View details
trnI-CAU-trnR-ACG IRb 4357 0.0454 0.99 78.7 yes View details
rrn16-rps12 IRb 2031 0.0428 1.00 81.6 yes View details
rpl32-trnP-GGG SSC 644 0.0864 1.00 84.8 yes View details
ndhG-ndhI SSC 338 0.0984 1.00 78.9 yes View details
rps12-rrn16 IRa 2031 0.0436 1.00 76.6 yes View details
trnR-ACG-ndhB IRa 3234 0.0543 0.99 78.0 yes View details
trnL-CAA-trnF-GAA LSC 416 0.0696 1.00 86.5 yes View details
psbE-petL LSC 1251 0.0625 0.99 85.7 yes View details
psbD-trnT-GGU LSC 1494 0.0615 1.00 85.0 yes View details
ndhC-trnV-UAC LSC 543 0.0652 1.00 84.9 yes View details
trnS-UGA-psbC LSC 846 0.0651 0.97 84.4 yes View details
rps4-trnL-CAA LSC 661 0.0562 0.94 82.9 yes View details
trnV-UAC-trnM-CAU LSC 222 0.0613 0.99 82.8 yes View details
ycf1-chlN SSC 475 0.0691 1.00 82.3 yes View details
accD-psaI LSC 466 0.0547 1.00 82.2 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-rps16_p1 matK-rps16 CTCGGACTTGTCGACGAAAT TGACTATCCTGATACGCCGT 1877–1991 0.625 76.6
matK-rps16_p2 matK-rps16 AGAACCGCTCCCCAAATTTT TGACTATCCTGATACGCCGT 1642–1756 0.375 65.6
matK-rps16_p3 matK-rps16 AGAACCGCTCCCCAAATTTT CCATGAACGAGGCAATACCA 1922–2037 0.250 57.8
matK-rps16_p4 matK-rps16 AAGAACCGCTCCCCAAATTT TGACTATCCTGATACGCCGT 1757 0.125 44.7
matK-rps16_p5 matK-rps16 AAGAACCGCTCCCCAAATTT CCATGAACGAGGCAATACCA 2038 0.125 44.6
trnG-UCC_p1 trnG-UCC ATACCTCGCTCGCAATTTGT GGAATTGGAAGCTTTCGCAC 1800–1841 0.750 79.8
trnG-UCC_p2 trnG-UCC ATACCTCGCTCGCAATTTGT AGAGACTGCGCGAATTACTG 1729–1770 0.750 79.4
trnG-UCC_p3 trnG-UCC ATACCTCGCTCGCAATTTGT CAGAGACTGCGCGAATTACT 1730–1771 0.750 79.4
trnG-UCC_p4 trnG-UCC ATACCTCGCTCGCAATTTGT ACTCAGAATCAGTTAGCGCG 1757–1795 0.625 71.0
trnG-UCC_p5 trnG-UCC ATACCTCGCTCGCAATTTGT CTTCGTCATATGGTGGGTGG 1227 0.125 44.4
atpH-atpI_p1 atpH-atpI TGTCTCGCAATGCCTTCTAC ACCAGGACTCAAATGGGAGA 1286–1316 1.000 91.3
atpH-atpI_p2 atpH-atpI TGTCTCGCAATGCCTTCTAC ACATCCAACCGACTCCAGTA 1039–1069 0.875 84.9
atpH-atpI_p3 atpH-atpI TGTCTCGCAATGCCTTCTAC AGTACATCCAACCGACTCCA 1042–1072 0.875 84.9
atpH-atpI_p4 atpH-atpI TGTCTCGCAATGCCTTCTAC TACATCCAACCGACTCCAGT 1040–1070 0.875 84.9
atpH-atpI_p5 atpH-atpI GTTTATGGTCTCGTCCCCAC ACCAGGACTCAAATGGGAGA 1613–1639 0.625 75.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GGGACTCCTCAGTACTTGGT AACCTTGGATTAGGCGACAC 1287–1321 0.875 85.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GGGACTCCTCAGTACTTGGT ATGGATGGTCAGTCGGAGAT 1615–1649 0.500 69.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TATGGTCTGATTCGCGGTTG ATGGATGGTCAGTCGGAGAT 1646–1680 0.500 69.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GATAAGGACCCTCGCGATTC ATGGATGGTCAGTCGGAGAT 1594–1628 0.500 69.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TGCATTGGGGTACAAATGCT ATGGATGGTCAGTCGGAGAT 1924–1958 0.500 69.1
trnE-UUC-trnG-GCC_p1 trnE-UUC-trnG-GCC CCTAGGCCTCTAGACGATGG GCGCGGATATAGTTGAATGG 759–797 1.000 79.0
trnE-UUC-trnG-GCC_p2 trnE-UUC-trnG-GCC CTAGGCCTCTAGACGATGGG GCGCGGATATAGTTGAATGG 758–796 1.000 79.0
trnE-UUC-trnG-GCC_p3 trnE-UUC-trnG-GCC CCTAGGCCTCTAGACGATGG GTTCGATTCCCGCTATCCG 707–745 1.000 78.8
trnE-UUC-trnG-GCC_p4 trnE-UUC-trnG-GCC CTAGGCCTCTAGACGATGGG GTTCGATTCCCGCTATCCG 706–744 1.000 78.8
trnE-UUC-trnG-GCC_p5 trnE-UUC-trnG-GCC CTAGGCCTCTAGACGATGGG GGTTCGATTCCCGCTATCC 707–745 1.000 78.6
trnS-UGA-psbC_p1 trnS-UGA-psbC GTTTGTACCATCCGATCCCC CGATACCGAACCCGTTCTTT 1303–1338 0.875 85.6
trnS-UGA-psbC_p2 trnS-UGA-psbC TGGCGTATTCGTTCCTCAAG CGATACCGAACCCGTTCTTT 1540–1575 0.500 69.4
trnS-UGA-psbC_p3 trnS-UGA-psbC ACGGATGAACATCGATGCAA CGATACCGAACCCGTTCTTT 1061–1095 0.500 69.1
trnS-UGA-psbC_p4 trnS-UGA-psbC TGGCGTATTCGTTCCTCAAG GTTTCTCCCCGAAGTTGGTT 1665–1700 0.500 68.5
trnS-UGA-psbC_p5 trnS-UGA-psbC TCCAGCACCCTAAGATCCAA CGATACCGAACCCGTTCTTT 1244–1259 0.375 61.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Lygodium circinatum NC_084180.1 158564 View on NCBI ↗
Lygodium flexuosum NC_084181.1 162109 View on NCBI ↗
Lygodium japonicum NC_022136.1 157260 View on NCBI ↗
Lygodium longifolium PQ591740.1 164439 View on NCBI ↗
Lygodium merrillii NC_084182.1 161997 View on NCBI ↗
Lygodium microphyllum NC_039378.1 158891 View on NCBI ↗
Lygodium polystachyum PQ591742.1 160902 View on NCBI ↗
Lygodium salicifolium PQ591741.1 162126 View on NCBI ↗