Markers + reference

Adiantum

5 species · Pteridaceae · Polypodiales

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Species 5
Genome length 150–155 kb
Candidate markers 267
Primer pairs 110

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 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
matK-rps16 LSC 802 0.2488 0.98 84.0 yes View details
rps16 LSC 663 0.2385 1.00 82.8 yes View details
atpH-atpI LSC 809 0.2464 0.97 82.7 yes View details
rpoB-trnD LSC 944 0.3140 0.93 81.1 yes View details
psbM-petN LSC 913 0.2822 0.93 81.6 yes View details
psbD-trnT LSC 1149 0.2345 0.97 83.2 yes View details
petA-psbJ LSC 743 0.2469 0.98 83.7 yes View details
rpl14-rpl16 LSC 445 0.3459 0.90 76.6 yes View details
rpl23 LSC 282 0.1897 1.00 72.5 yes View details
ndhF SSC 2190 0.1827 0.99 79.7 yes View details
rpl32-trnP SSC 661 0.3247 0.94 82.5 yes View details
rps4-trnL LSC 735 0.2184 0.98 84.6 yes View details
rpl20-rps12 LSC 951 0.1533 0.99 84.3 yes View details
rpl2 LSC 1565 0.1822 0.99 84.2 yes View details
petB LSC 1353 0.1449 1.00 84.0 yes View details
rpl16 LSC 1094 0.1464 0.98 83.9 yes View details
trnT-trnR IRb 912 0.1249 0.98 83.8 yes View details
trnR-trnT IRa 912 0.1246 0.99 83.8 yes View details
rps7-rps12 IRa 623 0.0551 1.00 83.4 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-rps16_p1 matK-rps16 GGTCACGTACGCTACCAATT CTGAACGGGTGGCATCATAA 1709 0.200 47.7
matK-rps16_p2 matK-rps16 GGTCACGTACGCTACCAATT CCACGTCGGATGTTACAAGT 1334 0.200 47.4
matK-rps16_p3 matK-rps16 GGTCACGTACGCTACCAATT ACTCCTATCAGGCTACCACC 1384 0.200 47.3
matK-rps16_p4 matK-rps16 GGTCACGTACGCTACCAATT CCGAAGCAATGTGGTAGGAA 1610 0.200 47.1
matK-rps16_p5 matK-rps16 GGTCACGTACGCTACCAATT GGAAGCGGCGTCAAATTAAC 1031 0.200 47.1
rps16_p1 rps16 TCTTCCACTTTTGCCTTCCC ACGTATTGACATCCCGTGTG 1496 0.200 47.9
rps16_p2 rps16 TCTTCCACTTTTGCCTTCCC CACGACACCAAGGGGATAAG 1327 0.200 47.8
rps16_p3 rps16 TCTTCCACTTTTGCCTTCCC CTGAACGGGTGGCATCATAA 1032 0.200 47.7
rps16_p4 rps16 TCTTCCACTTTTGCCTTCCC CAGGTTCAGGGTTTGTGTGA 1618 0.200 47.6
rps16_p5 rps16 TCTTCCACTTTTGCCTTCCC GGGTTACGAGGGAACGAATC 1418 0.200 47.4
trnG_p1 trnG CGGGACCGTTAGTAATTGCA TGTTTACGGAACAAGCGGAA 1630–1706 0.800 83.5
trnG_p2 trnG CGGGACCGTTAGTAATTGCA ATCAGTTCGACACATCAGCC 1590 0.200 47.8
trnG_p3 trnG TTGATTACCAGCCTCGCTTC ATCAGTTCGACACATCAGCC 1888 0.200 47.7
trnG_p4 trnG GGGGCTCCCTCTATACCAAT ATCAGTTCGACACATCAGCC 1465 0.200 47.5
trnG_p5 trnG TGATTGATTACCAGCCTCGC ATCAGTTCGACACATCAGCC 1891 0.200 47.5
atpH-atpI_p1 atpH-atpI CCCTCCTCGAAGGTTTTACG GTTGGTAGTAGCTGTTCCCG 1531 0.200 47.9
atpH-atpI_p2 atpH-atpI ATAACTCGAGGGAGCGATGA GTTGGTAGTAGCTGTTCCCG 1578 0.200 47.8
atpH-atpI_p3 atpH-atpI TAACTCGAGGGAGCGATGAT GTTGGTAGTAGCTGTTCCCG 1577 0.200 47.8
atpH-atpI_p4 atpH-atpI CCCTCCTCGAAGGTTTTACG ATTTTGGCTGACGAGTTGGT 1545 0.200 47.8
atpH-atpI_p5 atpH-atpI CCCTCCTCGAAGGTTTTACG TCTTTGCCACTTTAGCTGCA 1436 0.200 47.8
rpoB-trnD_p1 rpoB-trnD TGGTATACGCGAGAATCCCT ATTGTTACCCCTCCCGGTAA 1754 0.200 47.7
rpoB-trnD_p2 rpoB-trnD TGGTATACGCGAGAATCCCT CCGCTTCTAGCTAATCGGTC 2031 0.200 47.5
rpoB-trnD_p3 rpoB-trnD TCCCTGATCTGAAATTGCGG ATTGTTACCCCTCCCGGTAA 1777 0.200 47.4
rpoB-trnD_p4 rpoB-trnD TGATCCGACTCCCGATTGTA ATTGTTACCCCTCCCGGTAA 1731 0.200 47.3
rpoB-trnD_p5 rpoB-trnD TGGTATACGCGAGAATCCCT CGTTGCAATTTCCCGTATCG 1454 0.200 47.2
psbM-petN_p1 psbM-petN TCTTTACATTCAGACGGCCG CGTTTTCCCTCTCGCTTGTA 955–994 0.400 67.4
psbM-petN_p2 psbM-petN TCTTTACATTCAGACGGCCG TACGTTTTCCCTCTCGCTTG 957–996 0.400 67.4
psbM-petN_p3 psbM-petN TCTTTACATTCAGACGGCCG CAAGCGGTAAGACGTAGGAC 1525–1548 0.400 67.2
psbM-petN_p4 psbM-petN TCTCGATAGGACCGCTCAAT CGTTTTCCCTCTCGCTTGTA 1117 0.200 47.3
psbM-petN_p5 psbM-petN TCTCGATAGGACCGCTCAAT TACGTTTTCCCTCTCGCTTG 1119 0.200 47.3

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
Adiantum capillus-veneris NC_004766.1 150568 View on NCBI ↗
Adiantum flabellulatum NC_064144.1 152063 View on NCBI ↗
Adiantum malesianum NC_063331.1 154671 View on NCBI ↗
Adiantum reniforme var. sinense NC_062433.1 150102 View on NCBI ↗
Adiantum shastense NC_037478.1 150414 View on NCBI ↗