Markers + reference

Hymenasplenium

12 species · Aspleniaceae · Polypodiales

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Species 12
Genome length 152–152 kb
Candidate markers 207
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 207 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
matK-rps16 LSC 1195 0.0583 1.00 81.9 yes View details
trnS-GCU-ycf12 LSC 511 0.0650 0.99 82.2 yes View details
rpoC1-trnD-GUC LSC 4418 0.0288 1.00 63.3 yes View details
trnE-UUC-petN LSC 1325 0.0623 1.00 87.0 yes View details
psbD-trnT-GGU LSC 1212 0.0572 0.99 83.8 yes View details
ndhC-trnM-CAU LSC 1203 0.0561 0.99 84.9 yes View details
trnN-GUU-rpl21 SSC 2998 0.0448 0.99 76.5 yes View details
rpl32-trnP-GGG SSC 428 0.1110 0.92 78.2 yes View details
ccsA-ndhD SSC 404 0.0863 0.96 79.7 yes View details
ycf1 SSC 3939 0.0448 1.00 72.7 yes View details
ycf1-chlN SSC 1541 0.0598 1.00 78.9 yes View details
trnT-UGU-matK LSC 1926 0.0411 1.00 77.1 no View details
petN-trnC-GCA LSC 490 0.0544 1.00 84.0 yes View details
psbK-psbI LSC 590 0.0619 0.99 81.9 yes View details
ccsA-petG LSC 1173 0.0404 0.99 81.6 yes View details
rps16 LSC 1099 0.0435 0.98 81.4 yes View details
trnC-GCA-trnG-GCC LSC 441 0.0654 1.00 80.8 yes View details
rrn16S-trnI-GAU IRa 308 0.0621 0.98 80.5 yes View details
trnI-GAU-rrn16S IRb 308 0.0680 0.97 80.3 yes View details
rpl33-rpl20 LSC 553 0.0464 1.00 79.3 yes View details
psaC-ndhE SSC 345 0.0699 1.00 79.3 yes View details
trnQ-UUG-psbK LSC 338 0.0491 1.00 79.1 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-rps16_p1 matK-rps16 TCCTCTCCGAGACCAAAGTT TCAATGAGAACGAGCTCTGC 1990 0.083 43.2
matK-rps16_p2 matK-rps16 TTCCTCTCCGAGACCAAAGT TCAATGAGAACGAGCTCTGC 1991 0.083 43.2
matK-rps16_p3 matK-rps16 TCCTCTCCGAGACCAAAGTT AATGAGAACGAGCTCTGCTG 1988 0.083 43.2
matK-rps16_p4 matK-rps16 TCCTCTCCGAGACCAAAGTT CAATGAGAACGAGCTCTGCT 1989 0.083 43.2
matK-rps16_p5 matK-rps16 TTCCTCTCCGAGACCAAAGT AATGAGAACGAGCTCTGCTG 1989 0.083 43.2
rps16_p1 rps16 CTTCTTCCTCAGCACTCGAC GGGGGCATGATACCAAAGAG 2099–2118 0.417 64.7
rps16_p2 rps16 CTTCTTCCTCAGCACTCGAC TTCCTCTGGGATATCGACCC 2210–2229 0.417 64.4
rps16_p3 rps16 CTTCTTCCTCAGCACTCGAC CCTCTGGGATATCGACCCTT 2208–2227 0.417 64.4
rps16_p4 rps16 CACTCGACGGGATAGTACCT TTCCTCTGGGATATCGACCC 2198–2203 0.250 51.7
rps16_p5 rps16 CACTCGACGGGATAGTACCT GGGGGCATGATACCAAAGAG 2087–2092 0.250 51.7
trnQ-UUG-psbK_p1 trnQ-UUG-psbK CGAAGAAGCTCGATCCACAA CTAACTGCAGCTTGCCAAAC 1143–1151 0.500 64.1
trnQ-UUG-psbK_p2 trnQ-UUG-psbK CGAAGAAGCTCGATCCACAA CGTAAGGGAAGGGAATGAGC 1219–1227 0.250 52.6
trnQ-UUG-psbK_p3 trnQ-UUG-psbK CGAAGAAGCTCGATCCACAA GTAAGGGAAGGGAATGAGCG 1218–1226 0.250 52.6
trnQ-UUG-psbK_p4 trnQ-UUG-psbK TTCCAAAGTTCTATCCGCCG CGTAAGGGAAGGGAATGAGC 1300–1308 0.250 52.4
trnQ-UUG-psbK_p5 trnQ-UUG-psbK TTCCAAAGTTCTATCCGCCG GTAAGGGAAGGGAATGAGCG 1299–1307 0.250 52.4
psbK-psbI_p1 psbK-psbI GGGTCAACCAATTGAAGGGT GAGAGATGGCTGAGAGGTCT 1129–1152 1.000 88.5
psbK-psbI_p2 psbK-psbI GGGTCAACCAATTGAAGGGT CAGTTCTTCGGAGAGATGGC 1139–1152 0.500 65.1
psbK-psbI_p3 psbK-psbI GGGTCAACCAATTGAAGGGT GTTCTTCGGAGAGATGGCTG 1137–1150 0.500 65.1
psbK-psbI_p4 psbK-psbI CACTTCGGGTTTCCTGTCAA GTAACGTGATACCTGGGCAG 1487–1499 0.500 64.9
psbK-psbI_p5 psbK-psbI GGGTCAACCAATTGAAGGGT GTAACGTGATACCTGGGCAG 1249–1262 0.500 64.8
trnS-GCU-ycf12_p1 trnS-GCU-ycf12 AGACCTCTCAGCCATCTCTC AGTTGCACAATTATTTCTAGATTCA 546–565 1.000 50.2
trnS-GCU-ycf12_p2 trnS-GCU-ycf12 AGACCTCTCAGCCATCTCTC AAGTTGCACAATTATTTCTAGATTCA 547–566 1.000 50.2
trnS-GCU-ycf12_p3 trnS-GCU-ycf12 AGACCTCTCAGCCATCTCTC GTTGCACAATTATTTCTAGATTCA 545–564 1.000 50.2
trnS-GCU-ycf12_p4 trnS-GCU-ycf12 AGACCTCTCAGCCATCTCTC AGAAAGTTGCACAATTATTTCT 550–569 1.000 50.1
trnS-GCU-ycf12_p5 trnS-GCU-ycf12 AGACCTCTCAGCCATCTCTC AGAAAGTTGCACAATTATTTCTAGA 550–569 1.000 50.1
rpoC1-trnD-GUC_p1 rpoC1-trnD-GUC GAAGCAGAAAGGGGGAAACA TGATTTGAGTCTATGTAGTAATTGCT 304–311 0.500 31.1
rpoC1-trnD-GUC_p2 rpoC1-trnD-GUC ACGGGCATATTTCCACTTCC TGATTTGAGTCTATGTAGTAATTGCT 837–847 0.500 28.9
rpoC1-trnD-GUC_p3 rpoC1-trnD-GUC CAAGTTCTGGTAGTACGGGC TGATTTGAGTCTATGTAGTAATTGCT 851–861 0.500 28.8
rpoC1-trnD-GUC_p4 rpoC1-trnD-GUC GCAAGTTCTGGTAGTACGGG TGATTTGAGTCTATGTAGTAATTGCT 852–862 0.500 28.8
rpoC1-trnD-GUC_p5 rpoC1-trnD-GUC TCTGTGCTATCCGTCGTAGT TGATTTGAGTCTATGTAGTAATTGCT 502–507 0.333 22.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Hymenasplenium apogamum PQ187899.1 151930 View on NCBI ↗
Hymenasplenium chingii PQ187898.1 151742 View on NCBI ↗
Hymenasplenium excisum PQ187897.1 151779 View on NCBI ↗
Hymenasplenium furfuraceum PQ187895.1 151707 View on NCBI ↗
Hymenasplenium laterepens PQ187905.1 151725 View on NCBI ↗
Hymenasplenium murakami-hatanakae PQ187900.1 151892 View on NCBI ↗
Hymenasplenium obtusidentatum PQ187907.1 151798 View on NCBI ↗
Hymenasplenium retusulum PQ187912.1 151840 View on NCBI ↗
Hymenasplenium sinense PQ187911.1 151734 View on NCBI ↗
Hymenasplenium unilaterale NC_035856.1 151723 View on NCBI ↗
Hymenasplenium wangpeishanii PQ187902.1 151674 View on NCBI ↗
Hymenasplenium wuliangshanense PQ187894.1 151778 View on NCBI ↗