Markers + reference

Angiopteris

3 species · Marattiaceae · Marattiales

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Species 3
Genome length 153–154 kb
Candidate markers 283
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 283 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 466 0.0129 1.00 55.5 yes View details
rps16 LSC 1067 0.0019 1.00 54.0 yes View details
petA LSC 957 0.0035 1.00 48.5 yes View details
petG-trnW-CCA LSC 141 0.0047 1.00 38.7 yes View details
petD LSC 1124 0.0024 1.00 36.3 yes View details
trnI-CAU-trnL-CAA IRb 2518 0.0013 1.00 57.5 yes View details
rpl32-trnP-GGG SSC 409 0.0049 1.00 55.8 yes View details
trnL-CAA-trnI-CAU IRa 2518 0.0037 1.00 59.0 yes View details
ycf66 LSC 1054 0.0025 1.00 60.4 yes View details
trnK-UUU-rps16 LSC 597 0.0022 1.00 60.3 yes View details
psbD-trnT-GGU LSC 1344 0.0020 1.00 60.2 yes View details
rbcL LSC 1428 0.0019 1.00 59.9 yes View details
atpA LSC 1527 0.0013 1.00 59.5 yes View details
rpl16 LSC 1272 0.0010 1.00 59.5 yes View details
rps14-psaB LSC 209 0.0064 1.00 59.2 yes View details
clpP LSC 1825 0.0007 1.00 58.6 yes View details
ndhE SSC 303 0.0066 1.00 56.8 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
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TTCTGTTGAAGCTCCTTCCG 525–526 1.000 79.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT GTAACGCTCACAACTTCCCT 556–557 1.000 79.0
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACAATCCACTGCCTT GTAACGCTCACAACTTCCCT 569–570 1.000 79.0
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACAATCCACTGCCTT TTCTGTTGAAGCTCCTTCCG 538–539 1.000 79.0
trnH-GUG-psbA_p5 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC GTAACGCTCACAACTTCCCT 557–558 1.000 78.8
trnK-UUU_p1 trnK-UUU TCCCCTCTCTTTCCTTTCTCA ACCTCGGTCATTGTTCAAAT 2575 1.000 47.9
trnK-UUU_p2 trnK-UUU AGTTTCTCCCCTCTCTTTCCT ACCTCGGTCATTGTTCAAAT 2581 1.000 47.9
trnK-UUU_p3 trnK-UUU TCTCCCCTCTCTTTCCTTTCT ACCTCGGTCATTGTTCAAAT 2577 1.000 45.6
trnK-UUU_p4 trnK-UUU CCCCTCTCTTTCCTTTCTCA ACCTCGGTCATTGTTCAAAT 2574 1.000 43.3
trnK-UUU_p5 trnK-UUU GTTTCTCCCCTCTCTTTCCT ACCTCGGTCATTGTTCAAAT 2580 1.000 43.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAATCCCGTAGTCGCACTT AAAGGAGCTCAAACTACCGC 732–733 1.000 75.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAATCCCGTAGTCGCACTT GAGCTCAAACTACCGCAACT 728–729 1.000 75.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG AAAGGAGCTCAAACTACCGC 722–723 1.000 74.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GAGCTCAAACTACCGCAACT 718–719 1.000 74.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA AAAGGAGCTCAAACTACCGC 720–721 1.000 73.0
rps16_p1 rps16 AGGGACAAGGAATACTCCAT CTCTTGATGTGGTAAGAGTCGA 1262–1263 1.000 40.3
rps16_p2 rps16 AGGGACAAGGAATACTCCAT TCTCTTGATGTGGTAAGAGTCG 1263–1264 1.000 40.3
rps16_p3 rps16 AGGGACAAGGAATACTCCAT TGATGTGGTAAGAGTCGATGA 1258–1259 1.000 40.3
rps16_p4 rps16 AGGGACAAGGAATACTCCAT TCTTGATGTGGTAAGAGTCGA 1261–1262 1.000 40.3
rps16_p5 rps16 AGGGACAAGGAATACTCCAT CTTGATGTGGTAAGAGTCGATGA 1260–1261 1.000 40.3
atpA_p1 atpA AGGTTCAAATCCTATTGGACGT TGCACTCACGCATGATTGAT 1750 1.000 57.5
atpA_p2 atpA AGGTTCAAATCCTATTGGACGT TGAATTGCACTCACGCATGA 1755 1.000 55.8
atpA_p3 atpA AGGTTCAAATCCTATTGGACGT TTGCACTCACGCATGATTGA 1751 1.000 55.8
atpA_p4 atpA AGGTTCAAATCCTATTGGACGT ATGAATTGCACTCACGCATG 1756 1.000 55.1
atpA_p5 atpA AGGTTCAAATCCTATTGGACGT ATTGCACTCACGCATGATTG 1752 1.000 55.1
ycf66_p1 ycf66 TCTCATCCAAGATTAACTCCAAAGA AGAAAAGTCTATTCGAGATAGCCT 1185–1186 1.000 40.3
ycf66_p2 ycf66 TCTCATCCAAGATTAACTCCA AGAAAAGTCTATTCGAGATAGCCT 1185–1186 1.000 40.3
ycf66_p3 ycf66 TCTCATCCAAGATTAACTCCAA AGAAAAGTCTATTCGAGATAGCCT 1185–1186 1.000 40.3
ycf66_p4 ycf66 TTCTCATCCAAGATTAACTCCA AGAAAAGTCTATTCGAGATAGCCT 1186–1187 1.000 40.3
ycf66_p5 ycf66 CTCATCCAAGATTAACTCCAAAGA AGAAAAGTCTATTCGAGATAGCCT 1184–1185 1.000 40.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Angiopteris evecta NC_008829.1 153901 View on NCBI ↗
Angiopteris fokiensis NC_068854.1 153063 View on NCBI ↗
Angiopteris yunnanensis NC_052844.1 152962 View on NCBI ↗