Markers + reference

Marattia

2 species · Marattiaceae · Marattiales

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Species 2
Genome length 147–151 kb
Candidate markers 283
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 283 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf2 LSC 7149 0.0697 1.00 69.5 yes View details
trnH-GUG-psbA LSC 464 0.1341 0.71 73.3 yes View details
psbK-trnS-CGA LSC 420 0.0985 0.97 77.9 yes View details
psbZ-trnS-UGA LSC 395 0.0887 0.94 77.8 yes View details
trnT-GGU-trnfM-CAU LSC 1922 0.1431 0.26 61.5 yes View details
rps8-rpl14 LSC 446 0.1234 0.89 78.9 yes View details
trnL-CAA-ndhB IRb 2168 0.0756 0.70 72.3 yes View details
ycf1 SSC 4872 0.0563 1.00 67.6 yes View details
ndhD-ccsA SSC 341 0.1509 0.93 77.7 yes View details
trnP-GGG-rpl32 SSC 414 0.1003 0.87 76.4 yes View details
ndhF SSC 2316 0.0622 1.00 72.7 yes View details
ndhB-trnL-CAA IRa 2168 0.0756 0.70 72.3 yes View details
rpl20-rps12 LSC 921 0.0778 0.99 89.7 yes View details
psbM-trnD-GUC LSC 657 0.0842 0.99 82.9 yes View details
psbD-trnT-GGU LSC 1369 0.0856 0.98 80.3 yes View details
matK-trnK-UUU LSC 663 0.0501 0.96 80.2 yes View details
ndhC-trnV-UAC LSC 567 0.0861 0.96 80.0 yes View details
trnG-UCC-trnR-UCU LSC 199 0.1061 0.99 79.2 yes View details
clpP-psbB LSC 448 0.0851 0.94 78.7 yes View details
trnS-CGA-psbI LSC 224 0.0981 0.96 78.6 yes View details
trnD-GUC-trnY-GUA LSC 45 0.1778 1.00 78.2 yes View details
rps4-trnT-UGU LSC 239 0.1250 0.94 78.0 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
ycf2_p1 ycf2 TAGCTTCGGACGATCCAGAA CTTGGAACGGAGATCGACAC 750–760 1.000 81.0
ycf2_p2 ycf2 TCTTTCGGTCGGGAATAGGT CTTGGAACGGAGATCGACAC 578 0.500 55.9
ycf2_p3 ycf2 CGTCTTTCGGTCGGGAATAG CTTGGAACGGAGATCGACAC 580 0.500 55.7
ycf2_p4 ycf2 CTTTCGGTCGGGAATAGGTC CTTGGAACGGAGATCGACAC 577 0.500 55.3
ycf2_p5 ycf2 GTCTTTCGGTCGGGAATAGG CTTGGAACGGAGATCGACAC 579 0.500 55.3
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TTCCAAGCTGAGCACAACAT 871–1000 1.000 87.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CTGACGGTATGCCTCTAGGA 921–1050 1.000 87.7
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT GAGTGGGAACTTAGCTTCCG 1039–1168 1.000 87.4
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT GCCCGTAGTAGGTATCTGGT 722 0.500 58.9
trnH-GUG-psbA_p5 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TGGCCCGTAGTAGGTATCTG 724 0.500 58.9
matK-trnK-UUU_p1 matK-trnK-UUU TCCGAGATATTACATAGTGCA TCGGTCATCGTTCAAATGGG 725–748 1.000 46.1
matK-trnK-UUU_p2 matK-trnK-UUU TCCGAGATATTACATAGTGCAA TCGGTCATCGTTCAAATGGG 725–748 1.000 46.1
matK-trnK-UUU_p3 matK-trnK-UUU TCCGAGATATTACATAGTGCA TCTACCTCGGTCATCGTTCA 731–754 1.000 46.0
matK-trnK-UUU_p4 matK-trnK-UUU TCCGAGATATTACATAGTGCAA TCTACCTCGGTCATCGTTCA 731–754 1.000 46.0
matK-trnK-UUU_p5 matK-trnK-UUU TCCGAGATATTACATAGTGCAATCT TCTACCTCGGTCATCGTTCA 731–754 1.000 46.0
psbK-trnS-CGA_p1 psbK-trnS-CGA CGTGGATGTGATGCCAGTTA ATTCGAACCCTCGTTAACCG 571–582 1.000 87.9
psbK-trnS-CGA_p2 psbK-trnS-CGA ATGGCAAGCAGCTGTAAGTT ATTCGAACCCTCGTTAACCG 520–531 1.000 87.8
psbK-trnS-CGA_p3 psbK-trnS-CGA CGTGGATGTGATGCCAGTTA CTTTTTGGAGAGATGGCCGA 1069 1.000 86.2
psbK-trnS-CGA_p4 psbK-trnS-CGA CGTGGATGTGATGCCAGTTA TTTTTGGAGAGATGGCCGAG 1068 1.000 86.2
psbK-trnS-CGA_p5 psbK-trnS-CGA ACCTCCGAATAACAGGACCA ATTCGAACCCTCGTTAACCG 1033–1044 1.000 85.3
trnS-CGA-psbI_p1 trnS-CGA-psbI GGGTTCGAATCCCTCTTTCT ACCACTGTATAAACAAACAGCT 272–282 1.000 49.0
trnS-CGA-psbI_p2 trnS-CGA-psbI GGGTTCGAATCCCTCTTTCTC ACCACTGTATAAACAAACAGCT 272–282 1.000 49.0
trnS-CGA-psbI_p3 trnS-CGA-psbI GGTTCGAATCCCTCTTTCTCC ACCACTGTATAAACAAACAGCT 271–281 1.000 49.0
trnS-CGA-psbI_p4 trnS-CGA-psbI GGGTTCGAATCCCTCTTTCT ACCACTGTATAAACAAACAGCTT 272–282 1.000 49.0
trnS-CGA-psbI_p5 trnS-CGA-psbI GGGTTCGAATCCCTCTTTCT AACCACTGTATAAACAAACAGCT 273–283 1.000 48.9
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU ACCCTTAGCCTTCCAAGCTA TGTCCTATCCATTAGACGATGG 275–298 1.000 60.8
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU TAGTGATGCGGGTTCGATTC TGTCCTATCCATTAGACGATGG 257–280 1.000 59.7
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU CTAGTGATGCGGGTTCGATT TGTCCTATCCATTAGACGATGG 258–281 1.000 59.6
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU ACCCTTAGCCTTCCAAGCTA ATGTCCTATCCATTAGACGATGG 276–299 1.000 56.5
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTTAGCCTTCCAAGCTAG TGTCCTATCCATTAGACGATGG 274–297 1.000 56.0

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
Marattia cicutifolia NC_051978.1 151257 View on NCBI ↗
Marattia laxa NC_051979.1 147024 View on NCBI ↗