Markers + reference

Sphagnum

10 species · Sphagnaceae · Sphagnales

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Species 10
Genome length 139–140 kb
Candidate markers 270
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnI-CAU-rpl23 Genome 244 0.0183 1.00 44.8 yes View details
psaJ-trnP-UGG Genome 654 0.0190 1.00 61.6 yes View details
psbJ-petA Genome 1031 0.0238 1.00 64.3 yes View details
trnV-UAC-ndhC Genome 924 0.0202 0.98 66.7 yes View details
ndhJ-trnF-GAA Genome 448 0.0218 1.00 59.4 yes View details
trnT-GGU-trnE-UUC Genome 853 0.0167 0.99 62.8 yes View details
ycf2 Genome 7161 0.0100 1.00 43.0 yes View details
trnK-UUU-chlB Genome 1358 0.0229 0.99 63.2 yes View details
petN-ycf66 Genome 236 0.0426 0.96 68.1 yes View details
trnL-CAA-ndhB Genome 323 0.0446 0.99 73.6 yes View details
ycf66-psbM Genome 200 0.0272 0.99 74.8 yes View details
clpP-rps12 Genome 302 0.0203 0.94 71.0 yes View details
rrn23-trnA-UGC Genome 246 0.0244 1.00 71.0 yes View details
petN Genome 129 0.0446 1.00 67.3 yes View details
trnD-GUC-ycf2 Genome 682 0.0168 0.96 65.9 yes View details
psbD-trnT-GGU Genome 993 0.0136 1.00 65.8 yes View details
atpF-atpH Genome 350 0.0153 0.99 63.8 yes View details
rpoC1-rpoB Genome 26 0.0291 1.00 63.5 yes View details
rpl16-rpl14 Genome 169 0.0358 0.98 62.7 yes View details
trnP-GGG-rpl32 Genome 1043 0.0171 1.00 62.7 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
trnI-CAU-rpl23_p1 trnI-CAU-rpl23 GGTTCAACTCCTGTCGGATG ACCGGGTATTTCATTTCATCCA 288–304 1.000 64.3
trnI-CAU-rpl23_p2 trnI-CAU-rpl23 AGGTTCAACTCCTGTCGGAT ACCGGGTATTTCATTTCATCCA 289–305 1.000 63.6
trnI-CAU-rpl23_p3 trnI-CAU-rpl23 CGGTTAAAGCACCCAACTCA ACCGGGTATTTCATTTCATCCA 325–341 1.000 62.7
trnI-CAU-rpl23_p4 trnI-CAU-rpl23 TGGAGAATTCGCAGGTTCAA ACCGGGTATTTCATTTCATCCA 301–317 1.000 61.8
trnI-CAU-rpl23_p5 trnI-CAU-rpl23 TTGGAGAATTCGCAGGTTCA ACCGGGTATTTCATTTCATCCA 302–318 1.000 61.8
rpl16-rpl14_p1 rpl16-rpl14 CCGATAAAAATATGAGTGATGGGT CAGTTTTCGAGCCCCACTAT 243–252 1.000 48.8
rpl16-rpl14_p2 rpl16-rpl14 TCCGATAAAAATATGAGTGATGGGT CAGTTTTCGAGCCCCACTAT 244–253 1.000 48.8
rpl16-rpl14_p3 rpl16-rpl14 CCGATAAAAATATGAGTGATGGGT CGAGCCCCACTATTATCTGC 236–245 1.000 48.6
rpl16-rpl14_p4 rpl16-rpl14 TCCGATAAAAATATGAGTGATGGGT CGAGCCCCACTATTATCTGC 237–246 1.000 48.6
rpl16-rpl14_p5 rpl16-rpl14 TCCGATAAAAATATGAGTGATGGG CGAGCCCCACTATTATCTGC 237–246 1.000 48.6
clpP-rps12_p1 clpP-rps12 TGTCGGCAAAAGAAGCAAAA CGGTTGTCTTCGATTCCTGA 389–415 1.000 77.8
clpP-rps12_p2 clpP-rps12 TGTCGGCAAAAGAAGCAAAA CCCGAAGAGCTGGAGATTTT 423–449 1.000 77.3
clpP-rps12_p3 clpP-rps12 AGAGACGTTTTTATGTCGGCA CGGTTGTCTTCGATTCCTGA 402–428 1.000 77.0
clpP-rps12_p4 clpP-rps12 AGAGACGTTTTTATGTCGGCA CCCGAAGAGCTGGAGATTTT 436–462 1.000 76.5
clpP-rps12_p5 clpP-rps12 ATGTCGGCAAAAGAAGCAAA CGGTTGTCTTCGATTCCTGA 390–416 1.000 76.0
psaJ-trnP-UGG_p1 psaJ-trnP-UGG GGCGCCGTAGAAAGATATGT GGGATGACAGGATTCGAACC 761–775 1.000 83.6
psaJ-trnP-UGG_p2 psaJ-trnP-UGG GGCGCCGTAGAAAGATATGT AAAACAAACGCGCTACCAAG 724–738 1.000 83.3
psaJ-trnP-UGG_p3 psaJ-trnP-UGG GGCGCCGTAGAAAGATATGT CAGGGTAGGGATGACAGGAT 768–782 1.000 83.0
psaJ-trnP-UGG_p4 psaJ-trnP-UGG GGCGCCGTAGAAAGATATGT TTCAGGGTAGGGATGACAGG 770–784 1.000 82.9
psaJ-trnP-UGG_p5 psaJ-trnP-UGG TAAGCCAGCCAAAAATCCGA GGGATGACAGGATTCGAACC 801–815 0.900 78.7
psbJ-petA_p1 psbJ-petA AGGTACTGTAGCTGGTATCCT TCGAAAAAGTTCAATTAGCTGAGA 1144–1169 1.000 46.0
psbJ-petA_p2 psbJ-petA AGGTACTGTAGCTGGTATCCTT TCGAAAAAGTTCAATTAGCTGAGA 1144–1169 1.000 46.0
psbJ-petA_p3 psbJ-petA GGTACTGTAGCTGGTATCCTTG TCGAAAAAGTTCAATTAGCTGAGA 1143–1168 1.000 46.0
psbJ-petA_p4 psbJ-petA AGGTACTGTAGCTGGTATCCT CGAAAAAGTTCAATTAGCTGAGA 1143–1168 1.000 46.0
psbJ-petA_p5 psbJ-petA AGGTACTGTAGCTGGTATCCT TCGAAAAAGTTCAATTAGCTGAG 1144–1169 1.000 46.0
trnV-UAC-ndhC_p1 trnV-UAC-ndhC GGTTCGAATCCGTATAGCCC ATCATATTTGGCCAGTGGGG 968–992 1.000 83.6
trnV-UAC-ndhC_p2 trnV-UAC-ndhC TGCATGTTGGGTTCCTGAAA ATCATATTTGGCCAGTGGGG 1062–1087 1.000 83.0
trnV-UAC-ndhC_p3 trnV-UAC-ndhC CCGAGAATGTCTACGGTTCG ATCATATTTGGCCAGTGGGG 982–1006 1.000 82.7
trnV-UAC-ndhC_p4 trnV-UAC-ndhC CGGTTCGAATCCGTATAGCC ATCATATTTGGCCAGTGGGG 969–993 1.000 81.8
trnV-UAC-ndhC_p5 trnV-UAC-ndhC GGGTTCCTGAAACGGTTCAA ATCATATTTGGCCAGTGGGG 1054–1079 1.000 81.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Sphagnum fuscum PP820908.1 139046 View on NCBI ↗
Sphagnum junghuhnianum NC_060704.1 138947 View on NCBI ↗
Sphagnum magellanicum PP820909.1 138958 View on NCBI ↗
Sphagnum medium PP820907.1 140336 View on NCBI ↗
Sphagnum multifibrosum NC_060705.1 140417 View on NCBI ↗
Sphagnum nemoreum PP820905.1 139105 View on NCBI ↗
Sphagnum ovatum PP820903.1 140125 View on NCBI ↗
Sphagnum palustre NC_030198.1 140040 View on NCBI ↗
Sphagnum squarrosum PP820898.1 139024 View on NCBI ↗
Sphagnum subsecundum PP820897.1 140064 View on NCBI ↗