Markers + reference

Dicranopteris

2 species · Gleicheniaceae · Gleicheniales

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Species 2
Genome length 148–149 kb
Candidate markers 201
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 201 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
chlN SSC 1059 0.5050 0.85 80.9 yes View details
ycf1 SSC 4485 0.4874 0.84 75.2 yes View details
ndhH-ndhA SSC 427 0.5184 0.89 78.3 yes View details
ndhI SSC 576 0.5110 0.87 80.8 yes View details
ndhG SSC 597 0.4599 0.79 79.3 yes View details
ndhD SSC 1509 0.4923 0.86 81.0 yes View details
rpl32-trnN-GUU SSC 3452 0.4078 0.90 78.4 yes View details
ndhG-psaC SSC 851 0.4770 0.89 82.4 yes View details
ndhA SSC 1680 0.4710 0.86 80.7 yes View details
trnP-GGG-rpl32 SSC 1257 0.4807 0.84 80.6 yes View details
ndhH SSC 1203 0.4712 0.82 80.0 yes View details
ccsA SSC 966 0.4566 0.81 79.7 yes View details
chlL SSC 948 0.4974 0.80 79.4 yes View details
ndhD-ccsA SSC 282 0.4757 0.95 77.3 yes View details
chlN-ycf1 SSC 830 0.4628 0.71 76.9 yes View details
ccsA-trnL-UAG SSC 261 0.4407 0.90 76.1 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
chlL_p1 chlL TATAGGGGGAAGCGGTAGTG AGGGATTGACTCCACAGACA 2110 0.500 59.7
chlL_p2 chlL TATAGGGGGAAGCGGTAGTG AGATCGTAACTCCGAGAGCA 1534 0.500 59.6
chlL_p3 chlL AATAGAGGAATCTCCCCGGG AGGGATTGACTCCACAGACA 2337 0.500 59.5
chlL_p4 chlL AATAGAGGAATCTCCCCGGG AGATCGTAACTCCGAGAGCA 1761 0.500 59.4
chlL_p5 chlL GATAAACTCTTGAGGGGCGG AGGGATTGACTCCACAGACA 1852 0.500 59.4
chlN_p1 chlN TGCTCTCGGAGTTACGATCT CCCTGCACCACTCTGTATTC 1402 0.500 59.4
chlN_p2 chlN TGCTCTCGGAGTTACGATCT GCCAATACGGGACTTGGTAG 1913 0.500 59.3
chlN_p3 chlN TGCTCTCGGAGTTACGATCT TACAACGACATTCGAACGCT 1487 0.500 59.2
chlN_p4 chlN ACTCTCCCCTTTGAGTGTGA CCCTGCACCACTCTGTATTC 1539 0.500 58.9
chlN_p5 chlN TGCTCTCGGAGTTACGATCT CATTACGTGGGGTTTGACCA 1737 0.500 58.9
chlN-ycf1_p1 chlN-ycf1 AGCCCGATCTAGCCATTACT GTCTCCGTACGGGACTATCA 1313 0.500 59.5
chlN-ycf1_p2 chlN-ycf1 AGCCCGATCTAGCCATTACT TCTCCGTACGGGACTATCAC 1312 0.500 59.5
chlN-ycf1_p3 chlN-ycf1 AGCCCGATCTAGCCATTACT TGTCTCCGTACGGGACTATC 1314 0.500 59.5
chlN-ycf1_p4 chlN-ycf1 AGCCCGATCTAGCCATTACT TGTGTTGGTCGAACAAGGAG 1247 0.500 59.4
chlN-ycf1_p5 chlN-ycf1 AGCGTATGCATGAACCAGAG TCTCCGTACGGGACTATCAC 1330 0.500 59.2
ycf1_p1 ycf1 GGGACGAGTATTGGAACACC CCCCATTCATTCCCGCAATA 1096 0.500 59.8
ycf1_p2 ycf1 GGGGACGAGTATTGGAACAC CCCCATTCATTCCCGCAATA 1097 0.500 59.8
ycf1_p3 ycf1 GTGGGGACGAGTATTGGAAC CCCCATTCATTCCCGCAATA 1099 0.500 59.8
ycf1_p4 ycf1 GGGACGAGTATTGGAACACC AGGCTACTCCCCAAAATCCT 875 0.500 59.7
ycf1_p5 ycf1 GGGGACGAGTATTGGAACAC AGGCTACTCCCCAAAATCCT 876 0.500 59.7
ndhH_p1 ndhH GGATCCGCCGAATCTCAAAT CGTACATAGGGGATGGGACT 2242 0.500 59.0
ndhH_p2 ndhH GGATCCGCCGAATCTCAAAT TAGGGGATGGGACTCGATTC 2236 0.500 59.0
ndhH_p3 ndhH GGATCCGCCGAATCTCAAAT CGCATAAAGCCAGGGGTATT 2081 0.500 58.9
ndhH_p4 ndhH GGATCCGCCGAATCTCAAAT CATAGGGGATGGGACTCGAT 2238 0.500 58.6
ndhH_p5 ndhH GGATCCGCCGAATCTCAAAT CTGCTCGGACATTCTCTCAC 2265 0.500 58.4
ndhH-ndhA_p1 ndhH-ndhA GTTACGAGCTTCGGGGATTT CGTACATAGGGGATGGGACT 1220 0.500 59.8
ndhH-ndhA_p2 ndhH-ndhA GTTACGAGCTTCGGGGATTT TAGGGGATGGGACTCGATTC 1214 0.500 59.8
ndhH-ndhA_p3 ndhH-ndhA GTTACGAGCTTCGGGGATTT ATGTTGGTGTTCCTGACCAC 1360 0.500 59.7
ndhH-ndhA_p4 ndhH-ndhA GTTACGAGCTTCGGGGATTT CGCATAAAGCCAGGGGTATT 1059 0.500 59.7
ndhH-ndhA_p5 ndhH-ndhA GTTACGAGCTTCGGGGATTT CTCGGAGTTTGCATGATCCA 1646 0.500 59.6

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
Dicranopteris linearis NC_088765.1 148719 View on NCBI ↗
Dicranopteris pedata MN817664.1 148403 View on NCBI ↗