Markers + reference

Marsilea

2 species · Marsileaceae · Salviniales

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Species 2
Genome length 152–154 kb
Candidate markers 265
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhF Genome 2190 0.4967 0.84 79.0 yes View details
rpl32-trnP-GGG Genome 1049 0.5054 0.80 79.9 yes View details
trnL-UAG-ccsA Genome 400 0.5470 0.91 78.2 yes View details
ccsA Genome 972 0.4793 0.87 81.4 yes View details
ccsA-ndhD Genome 446 0.5238 0.80 76.3 yes View details
ndhD Genome 1509 0.4818 0.89 81.9 yes View details
ndhI Genome 570 0.4974 0.67 75.1 yes View details
ndhH Genome 1185 0.4948 0.82 79.9 yes View details
rps15 Genome 270 0.4734 0.63 68.2 yes View details
ycf1 Genome 4788 0.4836 0.82 74.0 yes View details
ndhG Genome 594 0.4818 0.92 82.7 yes View details
psbE-petL Genome 1219 0.0743 0.99 82.6 yes View details
chlL Genome 882 0.4774 0.90 82.5 yes View details
psbK-psbI Genome 636 0.0849 0.93 82.3 yes View details
chlN Genome 1368 0.4693 0.89 82.0 yes View details
ycf12-trnG-UCC Genome 139 0.1308 0.94 81.2 yes View details
rpl23-trnI-CAU Genome 239 0.1283 0.95 81.2 yes View details
trnS-UGA-psbC Genome 885 0.0815 0.98 80.5 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
psbK-psbI_p1 psbK-psbI CAGGCCGCGGTAAGTTTC CGTCCAGGATCGTTTGACAA 705–749 1.000 65.2
psbK-psbI_p2 psbK-psbI CAGGCCGCGGTAAGTTTC TTTACGTCCAGGATTCCGTC 721–765 1.000 61.5
psbK-psbI_p3 psbK-psbI CAGGCCGCGGTAAGTTTC CTTTACGTCCAGGATTCCGT 722–766 1.000 61.4
psbK-psbI_p4 psbK-psbI CAGGCCGCGGTAAGTTTC TCTTTACGTCCAGGATTCCG 723–767 1.000 59.1
psbK-psbI_p5 psbK-psbI CAGGCCGCGGTAAGTTTC GTCCAGGATCGTTTGACAAGA 704–748 1.000 58.6
ycf12-trnG-UCC_p1 ycf12-trnG-UCC TAGCAGCCCGTAAAGGAAAC AGACGAATCACACTTTTACCACT 201–204 1.000 65.1
ycf12-trnG-UCC_p2 ycf12-trnG-UCC TCGTATCGGGACCACTTGTA AGACGAATCACACTTTTACCACT 231–234 1.000 63.6
ycf12-trnG-UCC_p3 ycf12-trnG-UCC GCGCTAATAGTCGTATCGGG AGACGAATCACACTTTTACCACT 241–244 1.000 63.4
ycf12-trnG-UCC_p4 ycf12-trnG-UCC CGGGACCACTTGTAATTGCT AGACGAATCACACTTTTACCACT 225–228 1.000 63.4
ycf12-trnG-UCC_p5 ycf12-trnG-UCC GGCGCTAATAGTCGTATCGG AGACGAATCACACTTTTACCACT 242–245 1.000 63.3
trnS-UGA-psbC_p1 trnS-UGA-psbC ATGGTCGAGTGGTTTAAGGC CGTTCTTTCAATGACTCCCCT 996–1045 1.000 77.3
trnS-UGA-psbC_p2 trnS-UGA-psbC GGGTTCGAATCCCTCTCTCT CGTTCTTTCAATGACTCCCCT 936–985 1.000 76.9
trnS-UGA-psbC_p3 trnS-UGA-psbC CTTGAAAACTGGCATGGTGC CGTTCTTTCAATGACTCCCCT 970–1019 1.000 76.7
trnS-UGA-psbC_p4 trnS-UGA-psbC TCAGGAGAGATGGTCGAGTG CGTTCTTTCAATGACTCCCCT 1005–1054 1.000 76.2
trnS-UGA-psbC_p5 trnS-UGA-psbC ATGGTCGAGTGGTTTAAGGC ACCCGTTCTTTCAATGACTCC 999–1048 1.000 76.0
psbE-petL_p1 psbE-petL GTAATGCTGTGGATGACCCA GCGGATGTCAAAAAGGCAAA 1337–1353 1.000 81.3
psbE-petL_p2 psbE-petL GTTCTCCCGTATTCCCAGAC GCGGATGTCAAAAAGGCAAA 1282–1298 1.000 80.1
psbE-petL_p3 psbE-petL AGTAATGCTGTGGATGACCC GCGGATGTCAAAAAGGCAAA 1338–1354 1.000 78.9
psbE-petL_p4 psbE-petL AGGACGTTCTCCCGTATTCC GCGGATGTCAAAAAGGCAAA 1287–1303 1.000 77.8
psbE-petL_p5 psbE-petL TTCTCCCGTATTCCCAGACG GCGGATGTCAAAAAGGCAAA 1281–1297 1.000 77.8
rpl23-trnI-CAU_p1 rpl23-trnI-CAU ACTTGATTCTTTAGTCCATCCA TGGCGAATTCACAGGTTCAA 284–297 1.000 51.6
rpl23-trnI-CAU_p2 rpl23-trnI-CAU ACTTGATTCTTTAGTCCATCCA TTGGCGAATTCACAGGTTCA 285–298 1.000 51.5
rpl23-trnI-CAU_p3 rpl23-trnI-CAU ACTTGATTCTTTAGTCCATCCA AACGGTTAAAGCACCCAACT 310–323 1.000 50.6
rpl23-trnI-CAU_p4 rpl23-trnI-CAU ACTTGATTCTTTAGTCCATCCA TGAACGGTTAAAGCACCCAA 312–325 1.000 50.5
rpl23-trnI-CAU_p5 rpl23-trnI-CAU ACTTGATTCTTTAGTCCATCCA CATCCATGGCTGAACGGTTA 322–335 1.000 50.2
ndhF_p1 ndhF AGGGAGAGATATGTGGACGG CTTCTTTCCAAAGCAGGGGT 2744 0.500 60.0
ndhF_p2 ndhF GAGAGATATGTGGACGGGGA CTTCTTTCCAAAGCAGGGGT 2741 0.500 60.0
ndhF_p3 ndhF AGGGAGAGATATGTGGACGG CGGATCCGTGACAAATGAGT 2667 0.500 59.9
ndhF_p4 ndhF GAGAGATATGTGGACGGGGA CGGATCCGTGACAAATGAGT 2664 0.500 59.9
ndhF_p5 ndhF AGGGAGAGATATGTGGACGG AATGTTAACGTCGGACCTCG 2624 0.500 59.9

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
Marsilea crenata NC_022137.1 151628 View on NCBI ↗
Marsilea mutica PQ616049.1 154342 View on NCBI ↗