Markers + reference

Crepidomanes

2 species · Hymenophyllaceae · Hymenophyllales

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Species 2
Genome length 146–146 kb
Candidate markers 271
Primer pairs 90

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 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf2 Genome 5361 0.1700 0.98 74.4 yes View details
trnH-GUG-psbA Genome 351 0.3171 0.82 79.2 yes View details
psbA-matK Genome 601 0.2465 0.95 83.8 yes View details
matK-rps16 Genome 3826 0.2003 0.16 55.4 yes View details
trnE-UUC-trnG-GCC Genome 635 0.2476 0.83 85.9 yes View details
trnS-UGA-psbC Genome 753 0.2421 0.97 82.5 yes View details
rps8-rpl14 Genome 489 0.2455 0.67 75.0 yes View details
rpl32-trnP-GGG Genome 504 0.2774 0.82 78.3 yes View details
trnR-ACG-trnN-GUU Genome 434 0.1855 0.96 89.9 yes View details
trnN-GUU-trnR-ACG Genome 434 0.1855 0.96 89.9 yes View details
psbD-trnT-GGU Genome 1153 0.1732 0.95 85.9 yes View details
rps4-trnL-UAA Genome 805 0.1892 0.92 84.2 yes View details
trnV-GAC-rrn16 Genome 399 0.1929 0.99 84.0 yes View details
rrn16-trnV-GAC Genome 399 0.1929 0.99 84.0 yes View details
psbM-trnD-GUC Genome 452 0.2192 0.97 83.5 yes View details
ndhC-trnV-UAC Genome 578 0.2313 0.93 83.4 yes View details
trnP-GGG-trnL-UAG Genome 219 0.1981 0.95 82.8 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf2_p1 ycf2 TTGAGAGAGCTCGAATTGGC ACAGGATCGCAGTCTGTTTC 888 0.500 59.2
ycf2_p2 ycf2 AAGCCCTGATGCTATGCTTC ACAGGATCGCAGTCTGTTTC 583 0.500 59.1
ycf2_p3 ycf2 TTGAGAGAGCTCGAATTGGC TTGAATCGCTACAGGATCGC 898 0.500 58.7
ycf2_p4 ycf2 AAGCCCTGATGCTATGCTTC TTGAATCGCTACAGGATCGC 593 0.500 58.7
ycf2_p5 ycf2 GTTCGCAGCGATACACTGTA ACAGGATCGCAGTCTGTTTC 515 0.500 58.5
trnH-GUG-psbA_p1 trnH-GUG-psbA TTGCCTTAATCCACTTGGCT TGAAGCTCCTTCTGTAAACGG 358–404 1.000 78.9
trnH-GUG-psbA_p2 trnH-GUG-psbA TTGCCTTAATCCACTTGGCT GAAGCTCCTTCTGTAAACGGA 357–403 1.000 76.7
trnH-GUG-psbA_p3 trnH-GUG-psbA CGCGTAATGGATCCACAATC TGAAGCTCCTTCTGTAAACGG 380–426 1.000 76.1
trnH-GUG-psbA_p4 trnH-GUG-psbA TAATCCACTTGGCTACGTCC TGAAGCTCCTTCTGTAAACGG 352–398 1.000 75.9
trnH-GUG-psbA_p5 trnH-GUG-psbA TGCCTTAATCCACTTGGCTAC TGAAGCTCCTTCTGTAAACGG 357–403 1.000 75.7
psbA-matK_p1 psbA-matK TGCTCAGCCTGGAAAACAAT TTCAAGCCCCAATCATGCTT 1586–1599 1.000 89.2
psbA-matK_p2 psbA-matK TGCTCAGCCTGGAAAACAAT TTTCAAGCCCCAATCATGCT 1587–1600 1.000 89.2
psbA-matK_p3 psbA-matK GTGCTAGTGATCCAGTTGCA TTCAAGCCCCAATCATGCTT 1088–1101 1.000 89.1
psbA-matK_p4 psbA-matK AGAGGTTGCGGTTAAAAGGG TTCAAGCCCCAATCATGCTT 1155–1168 1.000 89.0
psbA-matK_p5 psbA-matK AGAGGTTGCGGTTAAAAGGG TTTCAAGCCCCAATCATGCT 1156–1169 1.000 89.0
matK-rps16_p1 matK-rps16 GAGTGCCAAATGAGCTCTCA TTGTCTAGCCACAAGATCGC 767 0.500 59.1
matK-rps16_p2 matK-rps16 AGCTCTCAACCCAGATGGAT TTGTCTAGCCACAAGATCGC 755 0.500 59.0
matK-rps16_p3 matK-rps16 GAGTGCCAAATGAGCTCTCA GCATCGTCCAAAGAGCCTAA 1115 0.500 59.0
matK-rps16_p4 matK-rps16 AGCTCTCAACCCAGATGGAT GCATCGTCCAAAGAGCCTAA 1103 0.500 58.9
matK-rps16_p5 matK-rps16 GAGTGCCAAATGAGCTCTCA GTGGAATAAGGCTTACGGCA 922 0.500 58.9
trnG-UCC_p1 trnG-UCC GCCATAAATAGCCAGGCTGT ACGGAACAAGCAGAAACCTT 2139–2174 1.000 90.9
trnG-UCC_p2 trnG-UCC GCCATAAATAGCCAGGCTGT AATTAGCAAGAGGTCAGCGG 2357–2392 1.000 90.8
trnG-UCC_p3 trnG-UCC GTTGCATCAGGACCGTTAGT ACGGAACAAGCAGAAACCTT 1697–1745 1.000 90.8
trnG-UCC_p4 trnG-UCC GTTGCATCAGGACCGTTAGT AATTAGCAAGAGGTCAGCGG 1915–1963 1.000 90.7
trnG-UCC_p5 trnG-UCC ACACTGGATTCCGGAGATGA AATTAGCAAGAGGTCAGCGG 1816–1864 1.000 90.6
psbM-trnD-GUC_p1 psbM-trnD-GUC AGTGCAGTAGCTATGAATGCA GCGCTCTAACCGATTGAACT 518–719 1.000 74.6
psbM-trnD-GUC_p2 psbM-trnD-GUC GTGCAGTAGCTATGAATGCA GCGCTCTAACCGATTGAACT 517–718 1.000 70.3
psbM-trnD-GUC_p3 psbM-trnD-GUC TGCAGTAGCTATGAATGCAAGA GCGCTCTAACCGATTGAACT 516–717 1.000 69.8
psbM-trnD-GUC_p4 psbM-trnD-GUC GAGTGCAGTAGCTATGAATGC GCGCTCTAACCGATTGAACT 519–720 1.000 69.8
psbM-trnD-GUC_p5 psbM-trnD-GUC AGTGCAGTAGCTATGAATGCA GGATTGACGGGTCTCGAAC 562–763 1.000 68.9

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
Crepidomanes latealatum NC_072291.1 145943 View on NCBI ↗
Crepidomanes minutum NC_063573.1 146474 View on NCBI ↗