Markers + reference

Schizaea

8 species · Schizaeaceae · Schizaeales

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Species 8
Genome length 150–165 kb
Candidate markers 245
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 245 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
NQW19_pgt001-NQW19_pgp082 Genome 589 0.2750 0.86 72.5 yes View details
NQW19_pgp074-NQW19_pgt004 Genome 1368 0.2329 0.81 72.2 yes View details
NQW19_pgp045 Genome 90945 0.0955 0.92 73.4 yes View details
NQW19_pgp005-NQW19_pgr004 Genome 3639 0.1265 0.76 67.1 yes View details
NQW19_pgp039 Genome 1461 0.1032 1.00 84.8 yes View details
NQW19_pgp027 Genome 1574 0.1214 1.00 84.6 yes View details
NQW19_pgp038 Genome 1169 0.1094 0.99 84.4 yes View details
NQW19_pgp031 Genome 1307 0.1237 0.99 84.3 yes View details
NQW19_pgp020-NQW19_pgt022 Genome 739 0.1076 0.98 84.3 yes View details
NQW19_pgp046-NQW19_pgp045 Genome 795 0.1295 0.96 83.8 yes View details
NQW19_pgp062-NQW19_pgp061 Genome 636 0.1163 0.99 83.5 yes View details
NQW19_pgp044-NQW19_pgp043 Genome 516 0.1493 1.00 83.4 yes View details
NQW19_pgp044 Genome 2010 0.1181 0.99 83.3 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
NQW19_pgt001-NQW19_pgp082_p1 NQW19_pgt001-NQW19_pgp082 CGGTTGTAGATGTGATGCCA ATCTACCCTCCGCTTAGACC 1450–1464 0.500 69.6
NQW19_pgt001-NQW19_pgp082_p2 NQW19_pgt001-NQW19_pgp082 CCAGAAGCTTACGCCATTCT ATCTACCCTCCGCTTAGACC 1475–1489 0.500 69.5
NQW19_pgt001-NQW19_pgp082_p3 NQW19_pgt001-NQW19_pgp082 GTTTCTCTCGCAAAACTGCC ATCTACCCTCCGCTTAGACC 1493–1507 0.500 69.4
NQW19_pgt001-NQW19_pgp082_p4 NQW19_pgt001-NQW19_pgp082 CTAGCTTTTGTGTGGCAAGC ATCTACCCTCCGCTTAGACC 1406–1420 0.500 69.4
NQW19_pgt001-NQW19_pgp082_p5 NQW19_pgt001-NQW19_pgp082 AGAAGCTTACGCCATTCTCG ATCTACCCTCCGCTTAGACC 1473–1487 0.500 69.1
NQW19_pgp074-NQW19_pgt004_p1 NQW19_pgp074-NQW19_pgt004 AACAAAGCGGTGGAATCCTT GCAGCCCAGGTTATGCTAAT 1992–2186 0.500 67.4
NQW19_pgp074-NQW19_pgt004_p2 NQW19_pgp074-NQW19_pgt004 AACAAAGCGGTGGAATCCTT ATGACGAGCCAGATCCCATA 2094–2288 0.500 67.3
NQW19_pgp074-NQW19_pgt004_p3 NQW19_pgp074-NQW19_pgt004 AACAAAGCGGTGGAATCCTT TATGACGAGCCAGATCCCAT 2110–2127 0.250 54.0
NQW19_pgp074-NQW19_pgt004_p4 NQW19_pgp074-NQW19_pgt004 AACAAAGCGGTGGAATCCTT TCTCCCTGCCTCGCAATATA 1654 0.125 44.9
NQW19_pgp074-NQW19_pgt004_p5 NQW19_pgp074-NQW19_pgt004 GAACCCCCTCTATGATCCGA TCTCCCTGCCTCGCAATATA 2004 0.125 44.8
NQW19_pgp062-NQW19_pgp061_p1 NQW19_pgp062-NQW19_pgp061 AGAACCGTTTTTCCCACTCC CGCGGAGACACTCATAAACA 1746–1755 0.625 72.5
NQW19_pgp062-NQW19_pgp061_p2 NQW19_pgp062-NQW19_pgp061 CGTAGACTAGCGCCACTTTT CGCGGAGACACTCATAAACA 1913–1922 0.625 72.3
NQW19_pgp062-NQW19_pgp061_p3 NQW19_pgp062-NQW19_pgp061 TTGAGCCAACTCTCATACGC CGCGGAGACACTCATAAACA 1958–1967 0.625 72.1
NQW19_pgp062-NQW19_pgp061_p4 NQW19_pgp062-NQW19_pgp061 CCCATGAGCCTTGGCAATAT CGCGGAGACACTCATAAACA 1786–1795 0.500 67.1
NQW19_pgp062-NQW19_pgp061_p5 NQW19_pgp062-NQW19_pgp061 CCCATGAGCCTTGGCAATAT ATCTCGTTCAACCTGGATGC 1683–1692 0.375 57.9
NQW19_pgp046-NQW19_pgp045_p1 NQW19_pgp046-NQW19_pgp045 AACAATCTCGAATGAGCCCC GTGTCATGGAAGCAGAGGAG 1438–1477 0.750 80.4
NQW19_pgp046-NQW19_pgp045_p2 NQW19_pgp046-NQW19_pgp045 TTTACTCTCTGCTGGTTCGC GTGTCATGGAAGCAGAGGAG 1465–1504 0.750 80.1
NQW19_pgp046-NQW19_pgp045_p3 NQW19_pgp046-NQW19_pgp045 CTCGGTATCCAAAATGGCCA GTGTCATGGAAGCAGAGGAG 1665–1694 0.625 72.5
NQW19_pgp046-NQW19_pgp045_p4 NQW19_pgp046-NQW19_pgp045 AACAATCTCGAATGAGCCCC AATCCATGTTCGAAGGACGG 1428 0.125 44.5
NQW19_pgp046-NQW19_pgp045_p5 NQW19_pgp046-NQW19_pgp045 CTCGGTATCCAAAATGGCCA AATCCATGTTCGAAGGACGG 1645 0.125 44.4
NQW19_pgp045_p1 NQW19_pgp045 ATCGACGCGTGATAAACCAA GGAAGACAAACTTTCGCACG 739 0.125 44.8
NQW19_pgp045_p2 NQW19_pgp045 CAATCCTCCTGCAAATCGGA GGAAGACAAACTTTCGCACG 1083 0.125 44.5
NQW19_pgp045_p3 NQW19_pgp045 TCCAATCCTCCTGCAAATCG GGAAGACAAACTTTCGCACG 1085 0.125 44.5
NQW19_pgp045_p4 NQW19_pgp045 AGGCTTACTGCATGGCTTTT GGAAGACAAACTTTCGCACG 913 0.125 44.3
NQW19_pgp045_p5 NQW19_pgp045 ATCGACGCGTGATAAACCAA GAGAACCTGGATAACCCCCT 1065 0.125 44.1
NQW19_pgp044_p1 NQW19_pgp044 CCGATTGTAACCACGAACCT CGAACCGAGGTGCAGAATAA 2938–2976 0.625 73.5
NQW19_pgp044_p2 NQW19_pgp044 GCGTCACACATACACCCTAG CGAACCGAGGTGCAGAATAA 2817–2854 0.500 66.1
NQW19_pgp044_p3 NQW19_pgp044 TTCTCTGCAGCAGTAGGAGT CGAACCGAGGTGCAGAATAA 2494–2502 0.250 52.8
NQW19_pgp044_p4 NQW19_pgp044 GGGGGATATTTCTCTGCAGC CGAACCGAGGTGCAGAATAA 2503–2511 0.250 52.6
NQW19_pgp044_p5 NQW19_pgp044 TTCTCTGCAGCAGTAGGAGT ACCTCCCCAAGACTTCGTTA 2793–2801 0.250 52.4

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
Schizaea dichotoma NC_065331.1 163675 View on NCBI ↗
Schizaea elegans NC_035807.1 156603 View on NCBI ↗
Schizaea fistulosa NC_065330.1 153147 View on NCBI ↗
Schizaea medusa NC_065329.1 163265 View on NCBI ↗
Schizaea pectinata NC_035808.1 156392 View on NCBI ↗
Schizaea poeppigiana NC_065332.1 160236 View on NCBI ↗
Schizaea pusilla NC_065502.1 149668 View on NCBI ↗
Schizaea sprucei NC_065333.1 165125 View on NCBI ↗