Markers + reference

Myriopteris

2 species · Pteridaceae · Polypodiales

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Species 2
Genome length 154–156 kb
Candidate markers 273
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
matK-rps16 LSC 707 0.1177 0.97 81.7 yes View details
trnS-GCU-psb30 LSC 706 0.1250 0.99 82.6 yes View details
petA-psbJ LSC 1012 0.1123 0.98 81.1 yes View details
trnN-GUU-ndhF SSC 2579 0.4954 0.84 78.4 yes View details
rpl32-trnP-GGG SSC 606 0.1151 0.98 81.1 yes View details
chlL-trnN-GUU IRa 745 0.1689 0.61 75.8 yes View details
psbD-trnT-GGU LSC 1186 0.0823 0.96 87.1 yes View details
psbK-psbI LSC 547 0.0996 0.97 85.7 yes View details
trnP-GGG-trnL-UAG SSC 188 0.1278 0.96 83.1 yes View details
ndhB-ndhB LSC 854 0.0812 0.98 82.0 no View details
rpoB-trnD-GUC LSC 862 0.0813 0.98 81.4 yes View details
trnS-GGA-rps4 LSC 450 0.1222 0.98 81.4 yes View details
ndhD-psaC SSC 167 0.1548 0.93 80.3 yes View details
psbM-petN LSC 927 0.0929 0.99 79.0 yes View details
trnY-GUA-trnE-UUC LSC 170 0.0610 0.96 78.6 yes View details
clpP1-psbB LSC 508 0.0701 0.98 78.6 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-rps16_p1 matK-rps16 CCTCAGAACCCAACTCGATG GGGTTCATCTTTGCATGCAC 1118 0.500 59.9
matK-rps16_p2 matK-rps16 CCTCAGAACCCAACTCGATG GGTTCATCTTTGCATGCACC 1117 0.500 59.9
matK-rps16_p3 matK-rps16 GTTTGGCCCATGTAATTGCC GGGTTCATCTTTGCATGCAC 1099 0.500 59.8
matK-rps16_p4 matK-rps16 GTTTGGCCCATGTAATTGCC GGTTCATCTTTGCATGCACC 1098 0.500 59.8
matK-rps16_p5 matK-rps16 CCTCAGAACCCAACTCGATG CGCACGAACTGAAACTTTCC 1155 0.500 59.7
psbK-psbI_p1 psbK-psbI CAAGCCGCAGTTAGTTTTCG TCCAAAAACGAAAAGCGAAACA 627–637 1.000 70.9
psbK-psbI_p2 psbK-psbI AGCCGCAGTTAGTTTTCGAT TCCAAAAACGAAAAGCGAAACA 625–635 1.000 70.6
psbK-psbI_p3 psbK-psbI AAGCCGCAGTTAGTTTTCGA TCCAAAAACGAAAAGCGAAACA 626–636 1.000 70.3
psbK-psbI_p4 psbK-psbI CAAGCCGCAGTTAGTTTTCG CCAAAAACGAAAAGCGAAACA 626–636 1.000 70.2
psbK-psbI_p5 psbK-psbI GCCAAGTTACCCGAAGCTTA TCCAAAAACGAAAAGCGAAACA 720–730 1.000 69.4
trnS-GCU-psb30_p1 trnS-GCU-psb30 GCAATCCGACGCTTTAAACC GCGAGTTGCGTAATTATTTCCA 771–806 1.000 70.0
trnS-GCU-psb30_p2 trnS-GCU-psb30 TAAACCTCTCGGCCATCTCT GCGAGTTGCGTAATTATTTCCA 757–792 1.000 69.6
trnS-GCU-psb30_p3 trnS-GCU-psb30 GCTTTAAACCTCTCGGCCAT GCGAGTTGCGTAATTATTTCCA 761–796 1.000 68.9
trnS-GCU-psb30_p4 trnS-GCU-psb30 TCCGACGCTTTAAACCTCTC GCGAGTTGCGTAATTATTTCCA 767–802 1.000 68.0
trnS-GCU-psb30_p5 trnS-GCU-psb30 GCAATCCGACGCTTTAAACC GCGAGTTGCGTAATTATTTCC 771–806 1.000 64.5
rpoB-trnD-GUC_p1 rpoB-trnD-GUC TGCAAGTTCTGGTAGTACGG GCGGTGCTCTAACCAATTGA 917–920 1.000 76.8
rpoB-trnD-GUC_p2 rpoB-trnD-GUC GCAAGTTCTGGTAGTACGGT GCGGTGCTCTAACCAATTGA 916–919 1.000 76.8
rpoB-trnD-GUC_p3 rpoB-trnD-GUC TTCGTGCAAGTTCTGGTAGT GCGGTGCTCTAACCAATTGA 921–924 1.000 75.5
rpoB-trnD-GUC_p4 rpoB-trnD-GUC TCGTGCAAGTTCTGGTAGTAC GCGGTGCTCTAACCAATTGA 920–923 1.000 72.4
rpoB-trnD-GUC_p5 rpoB-trnD-GUC TGCAAGTTCTGGTAGTACGG GGCGGTGCTCTAACCAATT 918–921 1.000 72.2
trnY-GUA-trnE-UUC_p1 trnY-GUA-trnE-UUC ATTTGATTGGGTCGAGCTGG CCAGGACACCTCTCTTTCAC 307–313 1.000 78.5
trnY-GUA-trnE-UUC_p2 trnY-GUA-trnE-UUC GATTGGGTCGAGCTGGATTC CCAGGACACCTCTCTTTCAC 303–309 1.000 77.2
trnY-GUA-trnE-UUC_p3 trnY-GUA-trnE-UUC CTGGATTCGAACCAGCGTAG CCAGGACACCTCTCTTTCAC 291–297 1.000 77.1
trnY-GUA-trnE-UUC_p4 trnY-GUA-trnE-UUC ATTTGATTGGGTCGAGCTGG CCCAGGACACCTCTCTTTCA 308–314 1.000 77.0
trnY-GUA-trnE-UUC_p5 trnY-GUA-trnE-UUC GATTGGGTCGAGCTGGATTC CCCAGGACACCTCTCTTTCA 304–310 1.000 75.7
psbM-petN_p1 psbM-petN AAACAGCCGCTCGGAATAAC CGTTTTCCCTCTCGCTTGTA 997–999 1.000 79.9
psbM-petN_p2 psbM-petN AAACAGCCGCTCGGAATAAC TACGTTTTCCCTCTCGCTTG 999–1001 1.000 79.9
psbM-petN_p3 psbM-petN CAAACAGCCGCTCGGAATAA CGTTTTCCCTCTCGCTTGTA 998–1000 1.000 79.9
psbM-petN_p4 psbM-petN CAAACAGCCGCTCGGAATAA TACGTTTTCCCTCTCGCTTG 1000–1002 1.000 79.9
psbM-petN_p5 psbM-petN TACATTCAAACAGCCGCTCG CGTTTTCCCTCTCGCTTGTA 1004–1006 1.000 79.8

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
Myriopteris lanosa PX893070.1 153924 View on NCBI ↗
Myriopteris lindheimeri NC_014592.1 155770 View on NCBI ↗